# HG changeset patch
# User iuc
# Date 1570744742 14400
# Node ID 3b1e7c170b10afe01883f962fbe85f32e60b52f6

"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"

diff -r 000000000000 -r 3b1e7c170b10 tb_variant_filter.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tb_variant_filter.xml	Thu Oct 10 17:59:02 2019 -0400
@@ -0,0 +1,160 @@
+<tool id="tb_variant_filter" name="TB Variant Filter" version="@TOOL_VERSION@+galaxy0" profile="16.04">
+    <description>M. tuberculosis H37Rv VCF filter</description>
+    <macros>
+        <token name="@TOOL_VERSION@">0.1.3</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">tb_variant_filter</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        tb_variant_filter
+        #if "region_filter" in str($filters).split(',')
+            #if str($filter_options.show_filter_options) == "yes":
+                --region_filter $filter_options.region_filter
+            #else
+                --region_filter pe_ppe,uvp
+            #end if
+        #end if
+        #if "close_to_indel_filter" in str($filters).split(',')
+            --close_to_indel_filter
+            #if str($filter_options.show_filter_options) == "yes":
+                --indel_window_size $filter_options.indel_window_size
+            #end if
+        #end if
+        #if "min_percentage_alt_filter" in str($filters).split(',') 
+            --min_percentage_alt_filter 
+            #if str($filter_options.show_filter_options) == "yes":
+                --min_percentage_alt $filter_options.min_percentage_alt
+            #end if
+        #end if
+        #if "min_depth_filter" in str($filters).split(',') 
+            --min_depth_filter 
+            #if str($filter_options.show_filter_options) == "yes":
+                --min_depth $filter_options.min_depth
+            #end if
+        #end if
+        #if "snv_only_filter" in str($filters).split(','):
+            --snv_only_filter
+        #end if
+        '$input1' '$output1'
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" label="VCF file to be filter"  format="vcf"/>
+
+        <param type="select" name="filters" multiple="true" label="Filters to apply">
+            <option value="region_filter" selected="true">Filter out variants by regions</option>
+            <option value="close_to_indel_filter">Filter variants close to indels</option>
+            <option value="min_percentage_alt_filter">Filter variants by percentage alt allele</option>
+            <option value="min_depth_filter">Filter sites by read alignment depth</option>
+            <option value="snv_only_filter">Only accept SNVs</option>
+        </param>
+
+        <conditional name="filter_options">
+            <param type="select" name="show_filter_options" label="Show options for the filters">
+                <option value="yes">Yes</option>
+                <option value="no" selected="true">No</option>
+            </param>
+            <when value="yes">
+                <param argument="--region_filter" type="select" multiple="true" label="Region filters to enable">
+                    <!-- if these are changed the code above needs to change to keep the defaults in line with those that are default here -->
+                    <option value="pe_ppe" selected="true">PE/PPE</option>
+                    <option value="tbprofiler">TBProfiler antibiotic resistant genes</option>
+                    <option value="mtbseq">MTBseq antibiotic resistant genes</option>
+                    <option value="uvp" selected="true">UVP repeat / insertion sequence sites</option>
+                </param>
+                <param argument="--indel_window_size" type="integer" value="5" label="Window to mask around indels"/>
+                <param argument="--min_percentage_alt" type="float" value="90"
+                    label="Minimum alternate allele percentage to accept"/>
+                <param argument="--min_depth" type="integer" value="30" label="Minimum read depth (coverage)"/>
+            </when>
+            <when value="no"></when>
+
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output1" format="vcf"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="test_input1.vcf" ftype="vcf" />
+            <param name="filters" value="region_filter" />
+            <conditional name="filter_options">
+                <param name="show_filter_options" value="yes" />
+                <param name="region_filter" value="pe_ppe,tbprofiler,uvp" />
+            </conditional>
+            <output name="output1" file="test_output1.vcf" ftype="vcf" />
+        </test>
+        <test>
+            <param name="input1" value="test_input1.vcf" ftype="vcf" />
+            <param name="filters" value="close_to_indel_filter" />
+            <conditional name="filter_options">
+                <param name="show_filter_options" value="yes" />
+                <param name="indel_window_size" value="5" />
+            </conditional>
+            <output name="output1" file="test_output2.vcf" ftype="vcf" />
+        </test>
+        <test>
+            <param name="input1" value="test_input1.vcf" ftype="vcf" />
+            <param name="filters" value="min_percentage_alt_filter" />
+            <conditional name="filter_options">
+                <param name="show_filter_options" value="yes" />
+                <param name="min_percentage_alt" value="95.0" />
+            </conditional>
+            <output name="output1" file="test_output3.vcf" ftype="vcf" />
+        </test>
+        <test>
+            <param name="input1" value="test_input2.vcf" ftype="vcf" />
+            <param name="filters" value="min_percentage_alt_filter" />
+            <conditional name="filter_options">
+                <param name="show_filter_options" value="yes" />
+                <param name="min_percentage_alt" value="30.0" />
+            </conditional>
+            <output name="output1" file="test_output4.vcf" ftype="vcf" />
+        </test>
+        <test>
+            <param name="input1" value="test_input1.vcf" ftype="vcf" />
+            <param name="filters" value="min_depth_filter" />
+            <conditional name="filter_options">
+                <param name="show_filter_options" value="yes" />
+                <param name="min_depth" value="30" />
+            </conditional>
+            <output name="output1" file="test_output5.vcf" ftype="vcf" />
+        </test>
+        <test>
+            <param name="input1" value="test_input1.vcf" ftype="vcf" />
+            <param name="filters" value="snv_only_filter" />
+            <output name="output1" file="test_output6.vcf" ftype="vcf" />
+        </test>
+    </tests>
+    <help><![CDATA[
+This tool offers multiple options for filtering variants (in
+VCF files, relative to M. tuberculosis H37Rv).
+
+It currently has 5 main modes:
+
+1. Filter by region. Mask out variants in certain regions. Region lists available as:
+    1.  PE/PPE genes from `Fishbein et al 2015 <https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.12981>`_
+    2. `TBProfiler <http://tbdr.lshtm.ac.uk/>`_ list of antibiotic resistant genes
+    3. `MTBseq <https://github.com/ngs-fzb/MTBseq_source>`_ list of antibiotic resistant genes
+    4. `UVP <https://github.com/CPTR-ReSeqTB/UVP>`_ list of repetitive loci in M. tuberculosis genome
+2. Filter by window around indels. Masks out variants within a certain distance (by default 5 bases) of an insertion or deletion site.
+3. Filter by percentage of alternate allele bases. Mask out variants with less than a minimum percentage (by default 90%) alternative alleles.
+4. Filter by depth of aligned reads.
+5. Filter out all variants that are not SNV (single nucleotide variants).
+
+When used together the effects of the filters are added (i.e. a variant is masked out if it is masked by any of the filters).
+    ]]></help>
+    <citations>
+        <citation type="bibtex"><![CDATA[
+@misc{vanHeusden2019,
+  author = {van Heusden, P.},
+  title = {tb_variant_filter},
+  year = {2019},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  howpublished = {\url{https://github.com/pvanheus/tb_variant_filter}},
+  commit = {4a9b2a4a85ddbfbb0d713a02373c8aa0aa159a6c}
+}
+        ]]></citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 3b1e7c170b10 test-data/test_input1.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_input1.vcf	Thu Oct 10 17:59:02 2019 -0400
@@ -0,0 +1,102 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20190323
+##source=freeBayes v1.2.0-dirty
+##reference=reference/ref.fa
+##contig=<ID=Chromosome,length=4411532>
+##phasing=none
+##commandline="freebayes -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam --region Chromosome:0-1495044"
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
+##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
+##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
+##bcftools_viewVersion=1.9+htslib-1.9
+##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=100.0 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Sat Mar 23 06:45:26 2019
+##bcftools_annotateVersion=1.9+htslib-1.9
+##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Sat Mar 23 06:45:26 2019
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	out
+Chromosome	1849	.	C	A	3412.24	.	AB=0;AO=110;DP=110;QA=3850;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:110:0:0:110:3850:-346.644,-33.1133,0
+Chromosome	1977	.	A	G	3234.43	.	AB=0;AO=106;DP=106;QA=3704;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:106:0:0:106:3704:-333.508,-31.9092,0
+Chromosome	4013	.	T	C	3965.91	.	AB=0;AO=125;DP=125;QA=4448;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:125:0:0:125:4448:-400.411,-37.6288,0
+Chromosome	7362	.	G	C	4009.71	.	AB=0;AO=126;DP=126;QA=4518;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:126:0:0:126:4518:-406.711,-37.9298,0
+Chromosome	9304	.	G	A	4222.23	.	AB=0;AO=136;DP=136;QA=4764;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:136:0:0:136:4764:-428.865,-40.9401,0
+Chromosome	11820	.	C	G	2252.54	.	AB=0;AO=74;DP=74;QA=2662;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:74:0:0:74:2662:-239.791,-22.2762,0
+Chromosome	11879	.	A	G	1815.99	.	AB=0;AO=63;DP=63;QA=2212;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:63:0:0:63:2212:-199.306,-18.9649,0
+Chromosome	14785	.	T	C	4342.4	.	AB=0;AO=139;DP=139;QA=4874;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:139:0:0:139:4874:-438.763,-41.8432,0
+Chromosome	14861	.	G	T	4237.79	.	AB=0;AO=133;DP=135;QA=4758;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:135:0:0:133:4758:-427.969,-40.037,0
+Chromosome	15117	.	C	G	3298.26	.	AB=0;AO=106;DP=106;QA=3708;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:106:0:0:106:3708:-333.903,-31.9092,0
+Chromosome	15890	.	G	A	3349.13	.	AB=0;AO=116;DP=117;QA=3770;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:117:0:0:116:3770:-339.321,-34.9195,0
+Chromosome	16119	.	C	A	3794.09	.	AB=0;AO=124;DP=125;QA=4268;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:125:0:0:124:4268:-383.905,-37.3277,0
+Chromosome	21795	.	G	A	768.571	.	AB=0;AO=28;DP=28;QA=892;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:892:-80.5646,-8.42884,0
+Chromosome	25610	.	G	C	2779.82	.	AB=0;AO=89;DP=89;QA=3137;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:89:0:0:89:3137:-282.515,-26.7917,0
+Chromosome	26959	.	C	G	2791.1	.	AB=0;AO=91;DP=91;QA=3152;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:91:0:0:91:3152:-283.856,-27.3937,0
+Chromosome	27455	.	T	C	1646.76	.	AB=0;AO=52;DP=52;QA=1868;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:52:0:0:52:1868:-168.374,-15.6536,0
+Chromosome	28366	.	AT	A	2447.14	.	AB=0;AO=82;DP=84;QA=2764;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:84:0:0:82:2764:-248.651,-24.6845,0
+Chromosome	34044	.	T	C	3866.76	.	AB=0;AO=122;DP=122;QA=4351;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:122:0:0:122:4351:-391.712,-36.7257,0
+Chromosome	36008	.	G	C	2942.73	.	AB=0;AO=98;DP=101;QA=3356;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:101:0:0:98:3356:-301.935,-29.5009,0
+Chromosome	37031	.	C	G	3922.6	.	AB=0;AO=128;DP=129;QA=4437;QR=34;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:129:1:34:128:4437:-396.072,-35.434,0
+Chromosome	37305	.	C	G	4975.87	.	AB=0;AO=157;DP=157;QA=5577;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:157:0:0:157:5577:-501.976,-47.2617,0
+Chromosome	39158	.	C	G	2017.05	.	AB=0;AO=66;DP=66;QA=2297;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:66:0:0:66:2297:-206.967,-19.868,0
+Chromosome	42281	.	C	A	996.941	.	AB=0;AO=33;DP=33;QA=1179;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:33:0:0:33:1179:-106.407,-9.93399,0
+Chromosome	42967	.	G	C	2851.59	.	AB=0;AO=92;DP=92;QA=3244;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:92:0:0:92:3244:-292.146,-27.6948,0
+Chromosome	43347	.	T	C	2847.24	.	AB=0;AO=92;DP=92;QA=3233;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:92:0:0:92:3233:-291.161,-27.6948,0
+Chromosome	44768	.	A	G	3099.48	.	AB=0;AO=99;DP=99;QA=3501;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:99:0:0:99:3501:-315.241,-29.802,0
+Chromosome	49360	.	C	T	2971.13	.	AB=0;AO=97;DP=97;QA=3365;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:97:0:0:97:3365:-303.059,-29.1999,0
+Chromosome	49690	.	GCC	G	3479.85	.	AB=0;AO=117;DP=117;QA=3917;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:117:0:0:117:3917:-352.709,-35.2205,0
+Chromosome	50557	.	T	C	3743.4	.	AB=0;AO=121;DP=121;QA=4203;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:121:0:0:121:4203:-378.409,-36.4246,0
+Chromosome	51949	.	A	G	3521.52	.	AB=0;AO=112;DP=112;QA=3955;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:112:0:0:112:3955:-356.092,-33.7154,0
+Chromosome	54394	.	A	G	3304.32	.	AB=0;AO=104;DP=105;QA=3711;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:105:0:0:104:3711:-333.937,-31.3071,0
+Chromosome	62049	.	A	G	2249.46	.	AB=0;AO=77;DP=78;QA=2659;QR=35;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:78:1:35:77:2659:-236.018,-19.9817,0
+Chromosome	63146	.	G	T	5120.15	.	AB=0;AO=163;DP=163;QA=5737;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:163:0:0:163:5737:-516.376,-49.0679,0
+Chromosome	65150	.	C	T	4046.85	.	AB=0;AO=134;DP=134;QA=4538;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:134:0:0:134:4538:-408.565,-40.338,0
+Chromosome	65246	.	C	T	3297.8	.	AB=0;AO=106;DP=107;QA=3712;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:107:0:0:106:3712:-334.038,-31.9092,0
+Chromosome	68337	.	T	TC	1791.13	.	AB=0;AO=60;DP=61;QA=2038;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:61:0:0:60:2038:-183.378,-18.0618,0
+Chromosome	69989	.	G	A	3539.46	.	AB=0;AO=119;DP=119;QA=3973;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:119:0:0:119:3973:-357.725,-35.8226,0
+Chromosome	70267	.	G	T	3018.85	.	AB=0;AO=100;DP=101;QA=3421;QR=25;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:101:1:25:100:3421:-305.576,-27.9042,0
+Chromosome	70816	.	A	G	4198.57	.	AB=0;AO=136;DP=136;QA=4707;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:136:0:0:136:4707:-423.747,-40.9401,0
+Chromosome	71336	.	G	C	556.161	.	AB=0;AO=21;DP=21;QA=770;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:770:-69.6143,-6.32163,0
+Chromosome	71914	.	T	C	3905.06	.	AB=0;AO=126;DP=126;QA=4382;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:126:0:0:126:4382:-394.523,-37.9298,0
+Chromosome	75233	.	C	A	1903.61	.	AB=0;AO=64;DP=64;QA=2172;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:64:0:0:64:2172:-195.723,-19.2659,0
+Chromosome	75940	.	G	C	2674.83	.	AB=0;AO=89;DP=89;QA=3048;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:89:0:0:89:3048:-274.519,-26.7917,0
+Chromosome	87468	.	C	T	4061.4	.	AB=0;AO=126;DP=126;QA=4584;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:126:0:0:126:4584:-412.628,-37.9298,0
+Chromosome	92199	.	T	G	686.38	.	AB=0;AO=23;DP=23;QA=799;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:799:-72.2155,-6.92369,0
+Chromosome	94388	.	G	A	2922.87	.	AB=0;AO=95;DP=95;QA=3292;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:95:0:0:95:3292:-296.486,-28.5979,0
+Chromosome	99162	.	TCGGTGTGCG	T	2040.99	.	AB=0;AO=78;DP=78;QA=2358;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:78:0:0:78:2358:-212.453,-23.4803,0
+Chromosome	105139	.	C	A	3418.74	.	AB=0;AO=109;DP=110;QA=3888;QR=38;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:110:1:38:109:3888:-346.257,-29.316,0
+Chromosome	105736	.	T	C	1805.18	.	AB=0;AO=61;DP=61;QA=2101;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:61:0:0:61:2101:-189.335,-18.3628,0
+Chromosome	116000	.	T	G	3196.37	.	AB=0;AO=105;DP=105;QA=3605;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:105:0:0:105:3605:-324.628,-31.6082,0
+Chromosome	122109	.	A	G	3324.29	.	AB=0;AO=111;DP=111;QA=3735;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:111:0:0:111:3735:-336.329,-33.4143,0
+Chromosome	123454	.	C	T	4362.28	.	AB=0;AO=136;DP=137;QA=4894;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:137:0:0:136:4894:-440.321,-40.9401,0
+Chromosome	123520	.	T	C	3793.13	.	AB=0;AO=121;DP=121;QA=4262;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:121:0:0:121:4262:-383.682,-36.4246,0
+Chromosome	125711	.	GGTT	G	3140.7	.	AB=0;AO=105;DP=105;QA=3531;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:105:0:0:105:3531:-317.98,-31.6082,0
+Chromosome	125830	.	G	GA	2079.98	.	AB=0;AO=69;DP=72;QA=2347;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:72:0:0:69:2347:-211.164,-20.7711,0
+Chromosome	131174	.	T	TG	2854.04	.	AB=0;AO=97;DP=99;QA=3213;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:99:0:0:97:3213:-288.972,-29.1999,0
+Chromosome	133839	.	C	T	2457.55	.	AB=0;AO=78;DP=78;QA=2802;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:78:0:0:78:2802:-252.374,-23.4803,0
+Chromosome	134024	.	T	C	2242.53	.	AB=0;AO=72;DP=72;QA=2543;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:72:0:0:72:2543:-229.099,-21.6742,0
+Chromosome	138419	.	G	A	4166.36	.	AB=0;AO=132;DP=132;QA=4683;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:132:0:0:132:4683:-421.582,-39.736,0
+Chromosome	139297	.	G	T	3706.81	.	AB=0;AO=120;DP=120;QA=4165;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:120:0:0:120:4165:-374.978,-36.1236,0
+Chromosome	143207	.	T	C	2180.95	.	AB=0;AO=72;DP=72;QA=2523;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:72:0:0:72:2523:-227.3,-21.6742,0
+Chromosome	146087	.	T	C	4315.28	.	AB=0;AO=137;DP=137;QA=4844;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:137:0:0:137:4844:-436.07,-41.2411,0
+Chromosome	147262	.	G	T	3766.49	.	AB=0;AO=122;DP=122;QA=4228;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:122:0:0:122:4228:-380.649,-36.7257,0
+Chromosome	154283	.	T	C	4403.08	.	AB=0;AO=141;DP=141;QA=4941;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:141:0:0:141:4941:-444.791,-42.4452,0
+Chromosome	154990	.	G	T	4207.92	.	AB=0;AO=142;DP=143;QA=4724;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:143:0:0:142:4724:-424.969,-42.7463,0
+Chromosome	162151	.	GT	G	2208.67	.	AB=0;AO=81;DP=84;QA=2524;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:84:0:0:81:2524:-226.95,-24.3834,0
+Chromosome	163940	.	A	G	2507.97	.	AB=0;AO=80;DP=80;QA=2839;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:80:0:0:80:2839:-255.719,-24.0824,0
+Chromosome	166253	.	A	C	3141.13	.	AB=0;AO=102;DP=102;QA=3586;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:102:0:0:102:3586:-322.902,-30.7051,0
+Chromosome	177857	.	G	A	2984.02	.	AB=0;AO=98;DP=98;QA=3389;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:98:0:0:98:3389:-305.192,-29.5009,0
+Chromosome	188800	.	T	C	1887.67	.	AB=0;AO=64;DP=64;QA=2217;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:64:0:0:64:2217:-199.772,-19.2659,0
+Chromosome	190816	.	A	C	1715.49	.	AB=0;AO=57;DP=57;QA=2026;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:57:0:0:57:2026:-182.579,-17.1587,0
+Chromosome	194305	.	C	CGG	1602.78	.	AB=0;AO=58;DP=59;QA=1889;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:59:0:0:58:1889:-169.924,-17.4597,0
+Chromosome	2738274	.	A	C	511.15	.	AB=0;AO=18;DP=19;QA=633;QR=35;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:19:1:35:18:633:-53.7923,-2.22094,0
+Chromosome	3750185	.	CGAC	GGTG	1102.73	.	AB=0;AO=36;DP=36;QA=1255;QR=0;RO=0;TYPE=complex	GT:DP:RO:QR:AO:QA:GL	1/1:36:0:0:36:1255:-113.24,-10.8371,0
+Chromosome	3750193	.	G	A	1198.75	.	AB=0;AO=40;DP=40;QA=1367;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:40:0:0:40:1367:-123.307,-12.0412,0
diff -r 000000000000 -r 3b1e7c170b10 test-data/test_input2.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_input2.vcf	Thu Oct 10 17:59:02 2019 -0400
@@ -0,0 +1,60 @@
+##fileformat=VCFv4.1
+##fileDate=20150301
+##source=freeBayes v0.9.20-16-g3e35e72
+##reference=reference.fasta
+##phasing=none
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
+##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
+##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
+##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
+##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
+##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
+##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
+##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
+##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
+##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
+##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
+##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
+##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
+##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
+##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
+##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio.  Ratio between depth in samples with each called alternate allele and those without.">
+##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
+##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
+##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
+##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
+##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
+##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
+##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
+##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
+##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
+##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
+##INFO=<ID=technology.Illumina,Number=A,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from Illumina">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	BR_002	BR_004	BR_006	BR_009	BR_013	BR_015	BR_016	BR_021	BR_023	BR_024	BR_025	BR_028	BR_030	BR_031	BR_040	BR_041	BR_043	BR_046	BR_047	BR_048	WL_031	WL_032	WL_054	WL_056	WL_057	WL_058	WL_061	WL_064	WL_066	WL_067	WL_069	WL_070	WL_071	WL_072	WL_076	WL_077	WL_078	WL_079	WL_080	WL_081
+E2_L101	117	.	GG	AT	12920.7	.	AB=0.47191;ABP=4.84019;AC=6;AF=0.0810811;AN=74;AO=127;CIGAR=2X;DP=1915;DPB=1915;DPRA=1.03669;EPP=278.787;EPPR=3870.4;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=37;NUMALT=1;ODDS=8.14286;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=4199;QR=57663;RO=1781;RPL=0;RPP=278.787;RPPR=3870.4;RPR=127;RUN=1;SAF=0;SAP=278.787;SAR=127;SRF=0;SRP=3870.4;SRR=1781;TYPE=mnp;technology.Illumina=1	GT:DP:RO:QR:AO:QA:GL	0/1:63:34:1128:29:947:-298.563,0,-354.855	0/0:275:274:8575:0:0:0,-82.4822,-2963.46	0/0:16:16:550:0:0:0,-4.81648,-177.826	0/0:50:50:1549:0:0:0,-15.0515,-539.68	.	0/0:137:136:4316:0:0:0,-40.9401,-1476.57	0/0:15:15:517:0:0:0,-4.51545,-166.858	0/0:63:62:2127:0:0:0,-18.6639,-687.592	0/1:5:2:69:3:104:-32.1979,0,-21.0475	0/0:13:13:401:0:0:0,-3.91339,-140.389	0/0:21:21:682:0:0:0,-6.32163,-229.683	0/0:32:32:1082:0:0:0,-9.63296,-353.685	.	0/0:25:25:833:0:0:0,-7.52575,-275.278	0/0:45:45:1363:0:0:0,-13.5463,-482.942	0/0:39:39:1253:0:0:0,-11.7402,-425.057	0/0:49:49:1491:0:0:0,-14.7505,-526.459	0/0:14:14:436:0:0:0,-4.21442,-151.539	0/0:82:81:2406:0:0:0,-24.3834,-864.723	0/1:27:13:421:14:448:-144.499,0,-134.074	0/0:68:68:2110:0:0:0,-20.47,-734.156	0/0:16:16:518:0:0:0,-4.81648,-174.927	0/0:56:56:1847:0:0:0,-16.8577,-614.506	0/0:34:34:1160:0:0:0,-10.235,-376.705	0/1:25:16:551:9:311:-92.7994,0,-170.391	0/0:52:51:1692:0:0:0,-15.3525,-560.486	0/0:33:33:1085:0:0:0,-9.93399,-361.947	0/0:21:21:709:0:0:0,-6.32163,-232.126	0/0:106:105:3327:1:29:0,-21.0095,-1128.75	0/0:9:9:310:0:0:0,-2.70927,-100.234	0/0:22:22:716:0:0:0,-6.62266,-240.745	0/0:129:128:4337:0:0:0,-38.5318,-1414.47	0/0:149:148:4978:0:0:0,-44.5524,-1632.14	0/0:26:26:837:0:0:0,-7.82678,-283.629	.	0/0:7:7:237:0:0:0,-2.10721,-77.6617	0/0:13:13:429:0:0:0,-3.91339,-142.928	0/1:126:63:2125:63:2117:-656.871,0,-657.593	0/1:21:13:446:8:243:-79.8453,0,-138.147	0/0:31:31:1050:0:0:0,-9.33193,-342.807
+E2_L101	123	.	T	A	688.632	.	AB=0.411765;ABP=4.1599;AC=1;AF=0.0135135;AN=74;AO=7;CIGAR=1X;DP=1922;DPB=1922;DPRA=0.32126;EPP=18.2106;EPPR=4159.21;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=37;NUMALT=1;ODDS=8.46314;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=239;QR=63119;RO=1914;RPL=0;RPP=18.2106;RPPR=4159.21;RPR=7;RUN=1;SAF=0;SAP=18.2106;SAR=7;SRF=0;SRP=4159.21;SRR=1914;TYPE=snp;technology.Illumina=1	GT:DP:RO:QR:AO:QA:GL	0/0:63:63:2133:0:0:0,-18.9649,-696.24	0/0:275:274:8643:0:0:0,-82.4822,-2969.78	0/1:17:10:345:7:239:-72.7264,0,-106.266	0/0:50:50:1547:0:0:0,-15.0515,-539.5	.	0/0:137:137:4441:0:0:0,-41.2411,-1495.87	0/0:15:15:524:0:0:0,-4.51545,-167.491	0/0:63:63:2185:0:0:0,-18.9649,-700.918	0/0:5:5:152:0:0:0,-1.50515,-53.9786	0/0:13:13:429:0:0:0,-3.91339,-142.925	0/0:21:21:703:0:0:0,-6.32163,-231.577	0/0:32:32:1093:0:0:0,-9.63296,-354.673	.	0/0:25:25:869:0:0:0,-7.52575,-278.526	0/0:45:45:1355:0:0:0,-13.5463,-482.221	0/0:39:39:1328:0:0:0,-11.7402,-431.808	0/0:49:49:1561:0:0:0,-14.7505,-532.757	0/0:14:14:444:0:0:0,-4.21442,-152.263	0/0:82:82:2552:0:0:0,-24.6845,-885.917	0/0:27:27:861:0:0:0,-8.12781,-293.786	0/0:68:68:2195:0:0:0,-20.47,-741.8	0/0:16:16:548:0:0:0,-4.81648,-177.639	0/0:57:57:1937:0:0:0,-17.1587,-630.601	0/0:34:34:1191:0:0:0,-10.235,-379.496	0/0:25:25:869:0:0:0,-7.52575,-278.526	0/0:53:53:1791:0:0:0,-15.9546,-585.47	0/0:33:33:1143:0:0:0,-9.93399,-367.175	0/0:21:21:734:0:0:0,-6.32163,-234.383	0/0:106:106:3423:0:0:0,-31.9092,-1156.28	0/0:9:9:310:0:0:0,-2.70927,-100.234	0/0:22:22:757:0:0:0,-6.62266,-244.448	0/0:130:130:4441:0:0:0,-39.1339,-1439.89	0/0:151:151:5081:0:0:0,-45.4555,-1665.48	0/0:26:26:899:0:0:0,-7.82678,-289.224	.	0/0:7:7:244:0:0:0,-2.10721,-78.2996	0/0:13:13:445:0:0:0,-3.91339,-144.377	0/0:127:127:4180:0:0:0,-38.2308,-1392.41	0/0:21:21:712:0:0:0,-6.32163,-232.396	0/0:31:31:1054:0:0:0,-9.33193,-343.166
+E2_L101	125	.	C	T	110675	.	AB=0.558397;ABP=37.7557;AC=47;AF=0.635135;AN=74;AO=1064;CIGAR=1X;DP=1923;DPB=1923;DPRA=0.800123;EPP=2313.46;EPPR=1866.13;GTI=0;LEN=1;MEANALT=1.02941;MQM=60;MQMR=60;NS=37;NUMALT=1;ODDS=7.31554;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=32732;QR=26625;RO=858;RPL=0;RPP=2313.46;RPPR=1866.13;RPR=1064;RUN=1;SAF=0;SAP=2313.46;SAR=1064;SRF=0;SRP=1866.13;SRR=858;TYPE=snp;technology.Illumina=1	GT:DP:RO:QR:AO:QA:GL	0/1:63:29:919:34:1086:-351.067,0,-296.04	0/1:275:136:3998:139:4075:-1396.19,0,-1365.26	0/1:17:7:231:10:323:-104.267,0,-71.9963	0/0:50:50:1463:0:0:0,-15.0515,-531.939	.	0/1:137:73:2205:64:1932:-644.905,0,-741.47	0/1:15:6:206:9:301:-94.9006,0,-62.3614	0/1:63:14:477:49:1547:-512.541,0,-136.291	0/1:5:3:93:2:69:-21.0475,0,-31.1725	1/1:13:0:0:13:388:-139.212,-3.91339,0	1/1:21:0:0:21:616:-223.722,-6.32163,0	0/1:32:7:224:25:787:-261.493,0,-66.8418	.	1/1:25:0:0:25:815:-273.654,-7.52575,0	0/1:45:23:652:22:616:-218.165,0,-229.408	1/1:39:0:0:39:1185:-418.932,-11.7402,0	0/1:49:16:469:33:949:-334.932,0,-155.746	0/0:14:14:396:0:0:0,-4.21442,-147.916	1/1:82:0:0:82:2334:-866.31,-24.6845,0	0/1:27:14:431:13:389:-131.174,0,-142.961	1/1:68:0:0:68:2019:-725.97,-20.47,0	1/1:16:0:0:16:493:-172.669,-4.81648,0	0/1:57:2:58:55:1716:-577.549,0,-4.35015	1/1:34:0:0:34:1117:-372.828,-10.235,0	0/1:25:9:295:16:540:-169.396,0,-91.3433	0/1:53:26:837:27:880:-279.548,0,-267.677	1/1:33:0:0:33:1063:-359.964,-9.93399,0	0/1:21:12:397:9:297:-92.7309,0,-125.728	0/1:107:50:1484:57:1738:-580.482,0,-501.622	1/1:9:0:0:9:282:-97.6869,-2.70927,0	1/1:22:0:0:22:711:-240.294,-6.62266,0	0/1:130:57:1814:72:2337:-747.579,0,-580.516	0/0:151:150:4800:1:31:0,-34.3561,-1621.09	1/1:26:0:0:26:813:-281.46,-7.82678,0	.	1/1:7:0:0:7:223:-76.3831,-2.10721,0	1/1:13:0:0:13:425:-142.565,-3.91339,0	0/0:127:127:4112:0:0:0,-38.2308,-1386.3	0/1:21:12:387:9:297:-92.7307,0,-124.822	0/1:31:21:677:10:338:-101.416,0,-219.904
+E2_L101	189	.	GT	GA,AA	79493.6	.	AB=0.530648,0.564103;ABP=12.3275,4.40227;AC=27,1;AF=0.364865,0.0135135;AN=74;AO=711,22;CIGAR=1M1X,2X;DP=1947;DPB=1947;DPRA=1.2223,0.775155;EPP=1546.93,50.7827;EPPR=2623.98;GTI=0;LEN=1,2;MEANALT=1.2,2;MQM=59.9536,60;MQMR=59.9528;NS=37;NUMALT=2;ODDS=8.57375;PAIRED=1,1;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=26768,823;QR=45917;RO=1207;RPL=711,22;RPP=1546.93,50.7827;RPPR=2623.98;RPR=0,0;RUN=1,1;SAF=0,0;SAP=1546.93,50.7827;SAR=711,22;SRF=0;SRP=2623.98;SRR=1207;TYPE=snp,mnp;technology.Illumina=1,1	GT:DP:RO:QR:AO:QA:GL	0/1:63:29:1128:33,0:1297,0:-362.019,0,-314.829,-370.749,-324.763,-695.435	0/1:279:136:5023:143,0:5199,0:-1527.93,0,-1456.1,-1568.87,-1499.14,-3067.65	0/0:18:18:720:0,0:0,0:0,-5.41854,-209.126,-5.41854,-209.126,-209.126	0/0:50:50:1802:0,0:0,0:0,-15.0515,-562.43,-15.0515,-562.43,-562.43	.	0/0:140:140:5188:0,0:0,0:0,-42.1442,-1586.93,-42.1442,-1586.93,-1586.93	0/0:15:15:612:0,0:0,0:0,-4.51545,-175.417,-4.51545,-175.417,-175.417	0/1:63:14:556:49,0:1902,0:-544.414,0,-143.417,-548.629,-158.168,-706.402	0/0:7:7:255:0,0:0,0:0,-2.10721,-79.294,-2.10721,-79.294,-79.294	1/1:13:0:0:13,0:486,0:-148.079,-3.91339,0,-148.079,-3.91339,-148.079	0/1:21:10:377:11,0:413,0:-119.194,0,-107.957,-122.204,-111.268,-233.097	0/1:33:7:283:26,0:969,0:-285.557,0,-71.9094,-287.664,-79.7362,-367.003	.	0/1:26:19:720:7,0:270,0:-72.8033,0,-209.291,-78.5229,-211.398,-289.538	0/0:45:45:1610:0,0:0,0:0,-13.5463,-505.167,-13.5463,-505.167,-505.167	1/2:39:0:0:17,22:633,823:-431.573,-243.764,-238.646,-188.182,0,-181.559	0/1:49:16:571:33,0:1209,0:-358.342,0,-164.964,-363.158,-174.898,-537.697	0/0:14:14:515:0,0:0,0:0,-4.21442,-158.684,-4.21442,-158.684,-158.684	0/1:82:37:1340:45,0:1616,0:-481.016,0,-392.198,-492.154,-405.744,-897.538	0/1:27:14:522:13,0:489,0:-140.222,0,-151.186,-144.436,-155.1,-299.162	1/1:69:0:0:69,0:2506,0:-777.734,-20.7711,0,-777.734,-20.7711,-777.734	0/1:17:10:355:7,0:270,0:-75.5457,0,-107.162,-78.556,-109.269,-187.452	0/1:58:33:1252:25,0:989,0:-271.846,0,-359.488,-281.78,-367.013,-648.405	0/1:35:19:755:16,0:627,0:-174.228,0,-209.735,-179.947,-214.551,-394.104	0/1:26:9:351:17,0:680,0:-189.701,0,-96.1193,-192.41,-101.237,-293.254	0/0:53:53:2059:0,0:0,0:0,-15.9546,-609.511,-15.9546,-609.511,-609.511	0/0:33:32:1269:0,0:0,0:0,-9.63296,-370.162,-9.63296,-370.162,-370.162	0/1:21:12:477:9,0:365,0:-98.8929,0,-132.958,-102.505,-135.668,-237.771	0/1:107:52:1896:55,0:2071,0:-594.399,0,-554.667,-610.053,-571.224,-1180.91	0/1:9:7:281:2,0:50,0:-18.0366,0,-78.9529,-20.1438,-79.555,-99.4154	1/1:22:0:0:22,0:864,0:-254.067,-6.62266,0,-254.067,-6.62266,-254.067	0/1:131:57:2263:72,0:2808,0:-789.722,0,-620.658,-806.881,-642.332,-1449.1	0/0:152:150:5887:1,0:38,0:0,-34.038,-1717.85,-45.1545,-1718.15,-1729.26	0/1:27:14:534:13,0:512,0:-142.297,0,-152.267,-146.511,-156.181,-302.304	.	0/1:7:3:113:4,0:158,0:-44.4921,0,-32.4297,-45.3952,-33.6338,-78.6449	0/0:14:14:544:0,0:0,0:0,-4.21442,-161.298,-4.21442,-161.298,-161.298	0/0:129:127:4963:0,0:0,0:0,-38.2308,-1462.3,-38.2308,-1462.3,-1462.3	0/1:22:13:480:9,0:347,0:-96.9577,0,-140.907,-100.871,-143.616,-244.109	0/0:31:31:1216:0,0:0,0:0,-9.33193,-357.713,-9.33193,-357.713,-357.713
diff -r 000000000000 -r 3b1e7c170b10 test-data/test_output1.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_output1.vcf	Thu Oct 10 17:59:02 2019 -0400
@@ -0,0 +1,94 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20190323
+##source=freeBayes v1.2.0-dirty
+##reference=reference/ref.fa
+##contig=<ID=Chromosome,length=4411532>
+##phasing=none
+##commandline="freebayes -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam --region Chromosome:0-1495044"
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
+##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
+##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
+##bcftools_viewVersion=1.9+htslib-1.9
+##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=100.0 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Sat Mar 23 06:45:26 2019
+##bcftools_annotateVersion=1.9+htslib-1.9
+##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Sat Mar 23 06:45:26 2019
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	out
+Chromosome	1849	.	C	A	3412.24	.	AB=0.0;AO=110;DP=110;QA=3850;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:110:0:0:110:3850:-346.644,-33.1133,0.0
+Chromosome	1977	.	A	G	3234.43	.	AB=0.0;AO=106;DP=106;QA=3704;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:106:0:0:106:3704:-333.508,-31.9092,0.0
+Chromosome	4013	.	T	C	3965.91	.	AB=0.0;AO=125;DP=125;QA=4448;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:125:0:0:125:4448:-400.411,-37.6288,0.0
+Chromosome	11820	.	C	G	2252.54	.	AB=0.0;AO=74;DP=74;QA=2662;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:74:0:0:74:2662:-239.791,-22.2762,0.0
+Chromosome	11879	.	A	G	1815.99	.	AB=0.0;AO=63;DP=63;QA=2212;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:63:0:0:63:2212:-199.306,-18.9649,0.0
+Chromosome	14785	.	T	C	4342.4	.	AB=0.0;AO=139;DP=139;QA=4874;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:139:0:0:139:4874:-438.763,-41.8432,0.0
+Chromosome	14861	.	G	T	4237.79	.	AB=0.0;AO=133;DP=135;QA=4758;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:135:0:0:133:4758:-427.969,-40.037,0.0
+Chromosome	15117	.	C	G	3298.26	.	AB=0.0;AO=106;DP=106;QA=3708;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:106:0:0:106:3708:-333.903,-31.9092,0.0
+Chromosome	15890	.	G	A	3349.13	.	AB=0.0;AO=116;DP=117;QA=3770;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:117:0:0:116:3770:-339.321,-34.9195,0.0
+Chromosome	16119	.	C	A	3794.09	.	AB=0.0;AO=124;DP=125;QA=4268;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:125:0:0:124:4268:-383.905,-37.3277,0.0
+Chromosome	21795	.	G	A	768.571	.	AB=0.0;AO=28;DP=28;QA=892;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:892:-80.5646,-8.42884,0.0
+Chromosome	25610	.	G	C	2779.82	.	AB=0.0;AO=89;DP=89;QA=3137;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:89:0:0:89:3137:-282.515,-26.7917,0.0
+Chromosome	26959	.	C	G	2791.1	.	AB=0.0;AO=91;DP=91;QA=3152;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:91:0:0:91:3152:-283.856,-27.3937,0.0
+Chromosome	27455	.	T	C	1646.76	.	AB=0.0;AO=52;DP=52;QA=1868;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:52:0:0:52:1868:-168.374,-15.6536,0.0
+Chromosome	28366	.	AT	A	2447.14	.	AB=0.0;AO=82;DP=84;QA=2764;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:84:0:0:82:2764:-248.651,-24.6845,0.0
+Chromosome	34044	.	T	C	3866.76	.	AB=0.0;AO=122;DP=122;QA=4351;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:122:0:0:122:4351:-391.712,-36.7257,0.0
+Chromosome	36008	.	G	C	2942.73	.	AB=0.0;AO=98;DP=101;QA=3356;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:101:0:0:98:3356:-301.935,-29.5009,0.0
+Chromosome	37031	.	C	G	3922.6	.	AB=0.0;AO=128;DP=129;QA=4437;QR=34;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:129:1:34:128:4437:-396.072,-35.434,0.0
+Chromosome	37305	.	C	G	4975.87	.	AB=0.0;AO=157;DP=157;QA=5577;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:157:0:0:157:5577:-501.976,-47.2617,0.0
+Chromosome	39158	.	C	G	2017.05	.	AB=0.0;AO=66;DP=66;QA=2297;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:66:0:0:66:2297:-206.967,-19.868,0.0
+Chromosome	42281	.	C	A	996.941	.	AB=0.0;AO=33;DP=33;QA=1179;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:33:0:0:33:1179:-106.407,-9.93399,0.0
+Chromosome	42967	.	G	C	2851.59	.	AB=0.0;AO=92;DP=92;QA=3244;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:92:0:0:92:3244:-292.146,-27.6948,0.0
+Chromosome	43347	.	T	C	2847.24	.	AB=0.0;AO=92;DP=92;QA=3233;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:92:0:0:92:3233:-291.161,-27.6948,0.0
+Chromosome	44768	.	A	G	3099.48	.	AB=0.0;AO=99;DP=99;QA=3501;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:99:0:0:99:3501:-315.241,-29.802,0.0
+Chromosome	49360	.	C	T	2971.13	.	AB=0.0;AO=97;DP=97;QA=3365;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:97:0:0:97:3365:-303.059,-29.1999,0.0
+Chromosome	49690	.	GCC	G	3479.85	.	AB=0.0;AO=117;DP=117;QA=3917;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:117:0:0:117:3917:-352.709,-35.2205,0.0
+Chromosome	50557	.	T	C	3743.4	.	AB=0.0;AO=121;DP=121;QA=4203;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:121:0:0:121:4203:-378.409,-36.4246,0.0
+Chromosome	51949	.	A	G	3521.52	.	AB=0.0;AO=112;DP=112;QA=3955;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:112:0:0:112:3955:-356.092,-33.7154,0.0
+Chromosome	54394	.	A	G	3304.32	.	AB=0.0;AO=104;DP=105;QA=3711;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:105:0:0:104:3711:-333.937,-31.3071,0.0
+Chromosome	62049	.	A	G	2249.46	.	AB=0.0;AO=77;DP=78;QA=2659;QR=35;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:78:1:35:77:2659:-236.018,-19.9817,0.0
+Chromosome	63146	.	G	T	5120.15	.	AB=0.0;AO=163;DP=163;QA=5737;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:163:0:0:163:5737:-516.376,-49.0679,0.0
+Chromosome	65150	.	C	T	4046.85	.	AB=0.0;AO=134;DP=134;QA=4538;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:134:0:0:134:4538:-408.565,-40.338,0.0
+Chromosome	65246	.	C	T	3297.8	.	AB=0.0;AO=106;DP=107;QA=3712;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:107:0:0:106:3712:-334.038,-31.9092,0.0
+Chromosome	68337	.	T	TC	1791.13	.	AB=0.0;AO=60;DP=61;QA=2038;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:61:0:0:60:2038:-183.378,-18.0618,0.0
+Chromosome	69989	.	G	A	3539.46	.	AB=0.0;AO=119;DP=119;QA=3973;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:119:0:0:119:3973:-357.725,-35.8226,0.0
+Chromosome	70267	.	G	T	3018.85	.	AB=0.0;AO=100;DP=101;QA=3421;QR=25;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:101:1:25:100:3421:-305.576,-27.9042,0.0
+Chromosome	70816	.	A	G	4198.57	.	AB=0.0;AO=136;DP=136;QA=4707;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:136:0:0:136:4707:-423.747,-40.9401,0.0
+Chromosome	71336	.	G	C	556.161	.	AB=0.0;AO=21;DP=21;QA=770;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:770:-69.6143,-6.32163,0.0
+Chromosome	71914	.	T	C	3905.06	.	AB=0.0;AO=126;DP=126;QA=4382;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:126:0:0:126:4382:-394.523,-37.9298,0.0
+Chromosome	75233	.	C	A	1903.61	.	AB=0.0;AO=64;DP=64;QA=2172;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:64:0:0:64:2172:-195.723,-19.2659,0.0
+Chromosome	75940	.	G	C	2674.83	.	AB=0.0;AO=89;DP=89;QA=3048;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:89:0:0:89:3048:-274.519,-26.7917,0.0
+Chromosome	87468	.	C	T	4061.4	.	AB=0.0;AO=126;DP=126;QA=4584;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:126:0:0:126:4584:-412.628,-37.9298,0.0
+Chromosome	92199	.	T	G	686.38	.	AB=0.0;AO=23;DP=23;QA=799;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:799:-72.2155,-6.92369,0.0
+Chromosome	94388	.	G	A	2922.87	.	AB=0.0;AO=95;DP=95;QA=3292;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:95:0:0:95:3292:-296.486,-28.5979,0.0
+Chromosome	99162	.	TCGGTGTGCG	T	2040.99	.	AB=0.0;AO=78;DP=78;QA=2358;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:78:0:0:78:2358:-212.453,-23.4803,0.0
+Chromosome	116000	.	T	G	3196.37	.	AB=0.0;AO=105;DP=105;QA=3605;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:105:0:0:105:3605:-324.628,-31.6082,0.0
+Chromosome	122109	.	A	G	3324.29	.	AB=0.0;AO=111;DP=111;QA=3735;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:111:0:0:111:3735:-336.329,-33.4143,0.0
+Chromosome	123454	.	C	T	4362.28	.	AB=0.0;AO=136;DP=137;QA=4894;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:137:0:0:136:4894:-440.321,-40.9401,0.0
+Chromosome	123520	.	T	C	3793.13	.	AB=0.0;AO=121;DP=121;QA=4262;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:121:0:0:121:4262:-383.682,-36.4246,0.0
+Chromosome	125711	.	GGTT	G	3140.7	.	AB=0.0;AO=105;DP=105;QA=3531;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:105:0:0:105:3531:-317.98,-31.6082,0.0
+Chromosome	125830	.	G	GA	2079.98	.	AB=0.0;AO=69;DP=72;QA=2347;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:72:0:0:69:2347:-211.164,-20.7711,0.0
+Chromosome	131174	.	T	TG	2854.04	.	AB=0.0;AO=97;DP=99;QA=3213;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:99:0:0:97:3213:-288.972,-29.1999,0.0
+Chromosome	133839	.	C	T	2457.55	.	AB=0.0;AO=78;DP=78;QA=2802;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:78:0:0:78:2802:-252.374,-23.4803,0.0
+Chromosome	134024	.	T	C	2242.53	.	AB=0.0;AO=72;DP=72;QA=2543;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:72:0:0:72:2543:-229.099,-21.6742,0.0
+Chromosome	138419	.	G	A	4166.36	.	AB=0.0;AO=132;DP=132;QA=4683;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:132:0:0:132:4683:-421.582,-39.736,0.0
+Chromosome	139297	.	G	T	3706.81	.	AB=0.0;AO=120;DP=120;QA=4165;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:120:0:0:120:4165:-374.978,-36.1236,0.0
+Chromosome	143207	.	T	C	2180.95	.	AB=0.0;AO=72;DP=72;QA=2523;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:72:0:0:72:2523:-227.3,-21.6742,0.0
+Chromosome	146087	.	T	C	4315.28	.	AB=0.0;AO=137;DP=137;QA=4844;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:137:0:0:137:4844:-436.07,-41.2411,0.0
+Chromosome	147262	.	G	T	3766.49	.	AB=0.0;AO=122;DP=122;QA=4228;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:122:0:0:122:4228:-380.649,-36.7257,0.0
+Chromosome	154283	.	T	C	4403.08	.	AB=0.0;AO=141;DP=141;QA=4941;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:141:0:0:141:4941:-444.791,-42.4452,0.0
+Chromosome	154990	.	G	T	4207.92	.	AB=0.0;AO=142;DP=143;QA=4724;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:143:0:0:142:4724:-424.969,-42.7463,0.0
+Chromosome	162151	.	GT	G	2208.67	.	AB=0.0;AO=81;DP=84;QA=2524;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:84:0:0:81:2524:-226.95,-24.3834,0.0
+Chromosome	163940	.	A	G	2507.97	.	AB=0.0;AO=80;DP=80;QA=2839;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:80:0:0:80:2839:-255.719,-24.0824,0.0
+Chromosome	166253	.	A	C	3141.13	.	AB=0.0;AO=102;DP=102;QA=3586;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:102:0:0:102:3586:-322.902,-30.7051,0.0
+Chromosome	190816	.	A	C	1715.49	.	AB=0.0;AO=57;DP=57;QA=2026;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:57:0:0:57:2026:-182.579,-17.1587,0.0
+Chromosome	194305	.	C	CGG	1602.78	.	AB=0.0;AO=58;DP=59;QA=1889;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:59:0:0:58:1889:-169.924,-17.4597,0.0
+Chromosome	2738274	.	A	C	511.15	.	AB=0.0;AO=18;DP=19;QA=633;QR=35;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:19:1:35:18:633:-53.7923,-2.22094,0.0
diff -r 000000000000 -r 3b1e7c170b10 test-data/test_output2.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_output2.vcf	Thu Oct 10 17:59:02 2019 -0400
@@ -0,0 +1,101 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20190323
+##source=freeBayes v1.2.0-dirty
+##reference=reference/ref.fa
+##contig=<ID=Chromosome,length=4411532>
+##phasing=none
+##commandline="freebayes -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam --region Chromosome:0-1495044"
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
+##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
+##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
+##bcftools_viewVersion=1.9+htslib-1.9
+##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=100.0 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Sat Mar 23 06:45:26 2019
+##bcftools_annotateVersion=1.9+htslib-1.9
+##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Sat Mar 23 06:45:26 2019
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	out
+Chromosome	1849	.	C	A	3412.24	.	AB=0.0;AO=110;DP=110;QA=3850;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:110:0:0:110:3850:-346.644,-33.1133,0.0
+Chromosome	1977	.	A	G	3234.43	.	AB=0.0;AO=106;DP=106;QA=3704;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:106:0:0:106:3704:-333.508,-31.9092,0.0
+Chromosome	4013	.	T	C	3965.91	.	AB=0.0;AO=125;DP=125;QA=4448;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:125:0:0:125:4448:-400.411,-37.6288,0.0
+Chromosome	7362	.	G	C	4009.71	.	AB=0.0;AO=126;DP=126;QA=4518;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:126:0:0:126:4518:-406.711,-37.9298,0.0
+Chromosome	9304	.	G	A	4222.23	.	AB=0.0;AO=136;DP=136;QA=4764;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:136:0:0:136:4764:-428.865,-40.9401,0.0
+Chromosome	11820	.	C	G	2252.54	.	AB=0.0;AO=74;DP=74;QA=2662;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:74:0:0:74:2662:-239.791,-22.2762,0.0
+Chromosome	11879	.	A	G	1815.99	.	AB=0.0;AO=63;DP=63;QA=2212;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:63:0:0:63:2212:-199.306,-18.9649,0.0
+Chromosome	14785	.	T	C	4342.4	.	AB=0.0;AO=139;DP=139;QA=4874;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:139:0:0:139:4874:-438.763,-41.8432,0.0
+Chromosome	14861	.	G	T	4237.79	.	AB=0.0;AO=133;DP=135;QA=4758;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:135:0:0:133:4758:-427.969,-40.037,0.0
+Chromosome	15117	.	C	G	3298.26	.	AB=0.0;AO=106;DP=106;QA=3708;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:106:0:0:106:3708:-333.903,-31.9092,0.0
+Chromosome	15890	.	G	A	3349.13	.	AB=0.0;AO=116;DP=117;QA=3770;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:117:0:0:116:3770:-339.321,-34.9195,0.0
+Chromosome	16119	.	C	A	3794.09	.	AB=0.0;AO=124;DP=125;QA=4268;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:125:0:0:124:4268:-383.905,-37.3277,0.0
+Chromosome	21795	.	G	A	768.571	.	AB=0.0;AO=28;DP=28;QA=892;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:892:-80.5646,-8.42884,0.0
+Chromosome	25610	.	G	C	2779.82	.	AB=0.0;AO=89;DP=89;QA=3137;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:89:0:0:89:3137:-282.515,-26.7917,0.0
+Chromosome	26959	.	C	G	2791.1	.	AB=0.0;AO=91;DP=91;QA=3152;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:91:0:0:91:3152:-283.856,-27.3937,0.0
+Chromosome	27455	.	T	C	1646.76	.	AB=0.0;AO=52;DP=52;QA=1868;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:52:0:0:52:1868:-168.374,-15.6536,0.0
+Chromosome	28366	.	AT	A	2447.14	.	AB=0.0;AO=82;DP=84;QA=2764;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:84:0:0:82:2764:-248.651,-24.6845,0.0
+Chromosome	34044	.	T	C	3866.76	.	AB=0.0;AO=122;DP=122;QA=4351;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:122:0:0:122:4351:-391.712,-36.7257,0.0
+Chromosome	36008	.	G	C	2942.73	.	AB=0.0;AO=98;DP=101;QA=3356;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:101:0:0:98:3356:-301.935,-29.5009,0.0
+Chromosome	37031	.	C	G	3922.6	.	AB=0.0;AO=128;DP=129;QA=4437;QR=34;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:129:1:34:128:4437:-396.072,-35.434,0.0
+Chromosome	37305	.	C	G	4975.87	.	AB=0.0;AO=157;DP=157;QA=5577;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:157:0:0:157:5577:-501.976,-47.2617,0.0
+Chromosome	39158	.	C	G	2017.05	.	AB=0.0;AO=66;DP=66;QA=2297;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:66:0:0:66:2297:-206.967,-19.868,0.0
+Chromosome	42281	.	C	A	996.941	.	AB=0.0;AO=33;DP=33;QA=1179;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:33:0:0:33:1179:-106.407,-9.93399,0.0
+Chromosome	42967	.	G	C	2851.59	.	AB=0.0;AO=92;DP=92;QA=3244;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:92:0:0:92:3244:-292.146,-27.6948,0.0
+Chromosome	43347	.	T	C	2847.24	.	AB=0.0;AO=92;DP=92;QA=3233;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:92:0:0:92:3233:-291.161,-27.6948,0.0
+Chromosome	44768	.	A	G	3099.48	.	AB=0.0;AO=99;DP=99;QA=3501;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:99:0:0:99:3501:-315.241,-29.802,0.0
+Chromosome	49360	.	C	T	2971.13	.	AB=0.0;AO=97;DP=97;QA=3365;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:97:0:0:97:3365:-303.059,-29.1999,0.0
+Chromosome	49690	.	GCC	G	3479.85	.	AB=0.0;AO=117;DP=117;QA=3917;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:117:0:0:117:3917:-352.709,-35.2205,0.0
+Chromosome	50557	.	T	C	3743.4	.	AB=0.0;AO=121;DP=121;QA=4203;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:121:0:0:121:4203:-378.409,-36.4246,0.0
+Chromosome	51949	.	A	G	3521.52	.	AB=0.0;AO=112;DP=112;QA=3955;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:112:0:0:112:3955:-356.092,-33.7154,0.0
+Chromosome	54394	.	A	G	3304.32	.	AB=0.0;AO=104;DP=105;QA=3711;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:105:0:0:104:3711:-333.937,-31.3071,0.0
+Chromosome	62049	.	A	G	2249.46	.	AB=0.0;AO=77;DP=78;QA=2659;QR=35;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:78:1:35:77:2659:-236.018,-19.9817,0.0
+Chromosome	63146	.	G	T	5120.15	.	AB=0.0;AO=163;DP=163;QA=5737;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:163:0:0:163:5737:-516.376,-49.0679,0.0
+Chromosome	65150	.	C	T	4046.85	.	AB=0.0;AO=134;DP=134;QA=4538;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:134:0:0:134:4538:-408.565,-40.338,0.0
+Chromosome	65246	.	C	T	3297.8	.	AB=0.0;AO=106;DP=107;QA=3712;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:107:0:0:106:3712:-334.038,-31.9092,0.0
+Chromosome	68337	.	T	TC	1791.13	.	AB=0.0;AO=60;DP=61;QA=2038;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:61:0:0:60:2038:-183.378,-18.0618,0.0
+Chromosome	69989	.	G	A	3539.46	.	AB=0.0;AO=119;DP=119;QA=3973;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:119:0:0:119:3973:-357.725,-35.8226,0.0
+Chromosome	70267	.	G	T	3018.85	.	AB=0.0;AO=100;DP=101;QA=3421;QR=25;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:101:1:25:100:3421:-305.576,-27.9042,0.0
+Chromosome	70816	.	A	G	4198.57	.	AB=0.0;AO=136;DP=136;QA=4707;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:136:0:0:136:4707:-423.747,-40.9401,0.0
+Chromosome	71336	.	G	C	556.161	.	AB=0.0;AO=21;DP=21;QA=770;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:770:-69.6143,-6.32163,0.0
+Chromosome	71914	.	T	C	3905.06	.	AB=0.0;AO=126;DP=126;QA=4382;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:126:0:0:126:4382:-394.523,-37.9298,0.0
+Chromosome	75233	.	C	A	1903.61	.	AB=0.0;AO=64;DP=64;QA=2172;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:64:0:0:64:2172:-195.723,-19.2659,0.0
+Chromosome	75940	.	G	C	2674.83	.	AB=0.0;AO=89;DP=89;QA=3048;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:89:0:0:89:3048:-274.519,-26.7917,0.0
+Chromosome	87468	.	C	T	4061.4	.	AB=0.0;AO=126;DP=126;QA=4584;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:126:0:0:126:4584:-412.628,-37.9298,0.0
+Chromosome	92199	.	T	G	686.38	.	AB=0.0;AO=23;DP=23;QA=799;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:799:-72.2155,-6.92369,0.0
+Chromosome	94388	.	G	A	2922.87	.	AB=0.0;AO=95;DP=95;QA=3292;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:95:0:0:95:3292:-296.486,-28.5979,0.0
+Chromosome	99162	.	TCGGTGTGCG	T	2040.99	.	AB=0.0;AO=78;DP=78;QA=2358;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:78:0:0:78:2358:-212.453,-23.4803,0.0
+Chromosome	105139	.	C	A	3418.74	.	AB=0.0;AO=109;DP=110;QA=3888;QR=38;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:110:1:38:109:3888:-346.257,-29.316,0.0
+Chromosome	105736	.	T	C	1805.18	.	AB=0.0;AO=61;DP=61;QA=2101;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:61:0:0:61:2101:-189.335,-18.3628,0.0
+Chromosome	116000	.	T	G	3196.37	.	AB=0.0;AO=105;DP=105;QA=3605;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:105:0:0:105:3605:-324.628,-31.6082,0.0
+Chromosome	122109	.	A	G	3324.29	.	AB=0.0;AO=111;DP=111;QA=3735;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:111:0:0:111:3735:-336.329,-33.4143,0.0
+Chromosome	123454	.	C	T	4362.28	.	AB=0.0;AO=136;DP=137;QA=4894;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:137:0:0:136:4894:-440.321,-40.9401,0.0
+Chromosome	123520	.	T	C	3793.13	.	AB=0.0;AO=121;DP=121;QA=4262;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:121:0:0:121:4262:-383.682,-36.4246,0.0
+Chromosome	125711	.	GGTT	G	3140.7	.	AB=0.0;AO=105;DP=105;QA=3531;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:105:0:0:105:3531:-317.98,-31.6082,0.0
+Chromosome	125830	.	G	GA	2079.98	.	AB=0.0;AO=69;DP=72;QA=2347;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:72:0:0:69:2347:-211.164,-20.7711,0.0
+Chromosome	131174	.	T	TG	2854.04	.	AB=0.0;AO=97;DP=99;QA=3213;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:99:0:0:97:3213:-288.972,-29.1999,0.0
+Chromosome	133839	.	C	T	2457.55	.	AB=0.0;AO=78;DP=78;QA=2802;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:78:0:0:78:2802:-252.374,-23.4803,0.0
+Chromosome	134024	.	T	C	2242.53	.	AB=0.0;AO=72;DP=72;QA=2543;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:72:0:0:72:2543:-229.099,-21.6742,0.0
+Chromosome	138419	.	G	A	4166.36	.	AB=0.0;AO=132;DP=132;QA=4683;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:132:0:0:132:4683:-421.582,-39.736,0.0
+Chromosome	139297	.	G	T	3706.81	.	AB=0.0;AO=120;DP=120;QA=4165;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:120:0:0:120:4165:-374.978,-36.1236,0.0
+Chromosome	143207	.	T	C	2180.95	.	AB=0.0;AO=72;DP=72;QA=2523;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:72:0:0:72:2523:-227.3,-21.6742,0.0
+Chromosome	146087	.	T	C	4315.28	.	AB=0.0;AO=137;DP=137;QA=4844;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:137:0:0:137:4844:-436.07,-41.2411,0.0
+Chromosome	147262	.	G	T	3766.49	.	AB=0.0;AO=122;DP=122;QA=4228;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:122:0:0:122:4228:-380.649,-36.7257,0.0
+Chromosome	154283	.	T	C	4403.08	.	AB=0.0;AO=141;DP=141;QA=4941;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:141:0:0:141:4941:-444.791,-42.4452,0.0
+Chromosome	154990	.	G	T	4207.92	.	AB=0.0;AO=142;DP=143;QA=4724;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:143:0:0:142:4724:-424.969,-42.7463,0.0
+Chromosome	162151	.	GT	G	2208.67	.	AB=0.0;AO=81;DP=84;QA=2524;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:84:0:0:81:2524:-226.95,-24.3834,0.0
+Chromosome	163940	.	A	G	2507.97	.	AB=0.0;AO=80;DP=80;QA=2839;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:80:0:0:80:2839:-255.719,-24.0824,0.0
+Chromosome	166253	.	A	C	3141.13	.	AB=0.0;AO=102;DP=102;QA=3586;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:102:0:0:102:3586:-322.902,-30.7051,0.0
+Chromosome	177857	.	G	A	2984.02	.	AB=0.0;AO=98;DP=98;QA=3389;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:98:0:0:98:3389:-305.192,-29.5009,0.0
+Chromosome	188800	.	T	C	1887.67	.	AB=0.0;AO=64;DP=64;QA=2217;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:64:0:0:64:2217:-199.772,-19.2659,0.0
+Chromosome	190816	.	A	C	1715.49	.	AB=0.0;AO=57;DP=57;QA=2026;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:57:0:0:57:2026:-182.579,-17.1587,0.0
+Chromosome	194305	.	C	CGG	1602.78	.	AB=0.0;AO=58;DP=59;QA=1889;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:59:0:0:58:1889:-169.924,-17.4597,0.0
+Chromosome	2738274	.	A	C	511.15	.	AB=0.0;AO=18;DP=19;QA=633;QR=35;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:19:1:35:18:633:-53.7923,-2.22094,0.0
+Chromosome	3750185	.	CGAC	GGTG	1102.73	.	AB=0.0;AO=36;DP=36;QA=1255;QR=0;RO=0;TYPE=complex	GT:DP:RO:QR:AO:QA:GL	1/1:36:0:0:36:1255:-113.24,-10.8371,0.0
diff -r 000000000000 -r 3b1e7c170b10 test-data/test_output3.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_output3.vcf	Thu Oct 10 17:59:02 2019 -0400
@@ -0,0 +1,101 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20190323
+##source=freeBayes v1.2.0-dirty
+##reference=reference/ref.fa
+##contig=<ID=Chromosome,length=4411532>
+##phasing=none
+##commandline="freebayes -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam --region Chromosome:0-1495044"
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
+##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
+##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
+##bcftools_viewVersion=1.9+htslib-1.9
+##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=100.0 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Sat Mar 23 06:45:26 2019
+##bcftools_annotateVersion=1.9+htslib-1.9
+##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Sat Mar 23 06:45:26 2019
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	out
+Chromosome	1849	.	C	A	3412.24	.	AB=0.0;AO=110;DP=110;QA=3850;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:110:0:0:110:3850:-346.644,-33.1133,0.0
+Chromosome	1977	.	A	G	3234.43	.	AB=0.0;AO=106;DP=106;QA=3704;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:106:0:0:106:3704:-333.508,-31.9092,0.0
+Chromosome	4013	.	T	C	3965.91	.	AB=0.0;AO=125;DP=125;QA=4448;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:125:0:0:125:4448:-400.411,-37.6288,0.0
+Chromosome	7362	.	G	C	4009.71	.	AB=0.0;AO=126;DP=126;QA=4518;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:126:0:0:126:4518:-406.711,-37.9298,0.0
+Chromosome	9304	.	G	A	4222.23	.	AB=0.0;AO=136;DP=136;QA=4764;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:136:0:0:136:4764:-428.865,-40.9401,0.0
+Chromosome	11820	.	C	G	2252.54	.	AB=0.0;AO=74;DP=74;QA=2662;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:74:0:0:74:2662:-239.791,-22.2762,0.0
+Chromosome	11879	.	A	G	1815.99	.	AB=0.0;AO=63;DP=63;QA=2212;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:63:0:0:63:2212:-199.306,-18.9649,0.0
+Chromosome	14785	.	T	C	4342.4	.	AB=0.0;AO=139;DP=139;QA=4874;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:139:0:0:139:4874:-438.763,-41.8432,0.0
+Chromosome	14861	.	G	T	4237.79	.	AB=0.0;AO=133;DP=135;QA=4758;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:135:0:0:133:4758:-427.969,-40.037,0.0
+Chromosome	15117	.	C	G	3298.26	.	AB=0.0;AO=106;DP=106;QA=3708;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:106:0:0:106:3708:-333.903,-31.9092,0.0
+Chromosome	15890	.	G	A	3349.13	.	AB=0.0;AO=116;DP=117;QA=3770;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:117:0:0:116:3770:-339.321,-34.9195,0.0
+Chromosome	16119	.	C	A	3794.09	.	AB=0.0;AO=124;DP=125;QA=4268;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:125:0:0:124:4268:-383.905,-37.3277,0.0
+Chromosome	21795	.	G	A	768.571	.	AB=0.0;AO=28;DP=28;QA=892;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:892:-80.5646,-8.42884,0.0
+Chromosome	25610	.	G	C	2779.82	.	AB=0.0;AO=89;DP=89;QA=3137;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:89:0:0:89:3137:-282.515,-26.7917,0.0
+Chromosome	26959	.	C	G	2791.1	.	AB=0.0;AO=91;DP=91;QA=3152;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:91:0:0:91:3152:-283.856,-27.3937,0.0
+Chromosome	27455	.	T	C	1646.76	.	AB=0.0;AO=52;DP=52;QA=1868;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:52:0:0:52:1868:-168.374,-15.6536,0.0
+Chromosome	28366	.	AT	A	2447.14	.	AB=0.0;AO=82;DP=84;QA=2764;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:84:0:0:82:2764:-248.651,-24.6845,0.0
+Chromosome	34044	.	T	C	3866.76	.	AB=0.0;AO=122;DP=122;QA=4351;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:122:0:0:122:4351:-391.712,-36.7257,0.0
+Chromosome	36008	.	G	C	2942.73	.	AB=0.0;AO=98;DP=101;QA=3356;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:101:0:0:98:3356:-301.935,-29.5009,0.0
+Chromosome	37031	.	C	G	3922.6	.	AB=0.0;AO=128;DP=129;QA=4437;QR=34;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:129:1:34:128:4437:-396.072,-35.434,0.0
+Chromosome	37305	.	C	G	4975.87	.	AB=0.0;AO=157;DP=157;QA=5577;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:157:0:0:157:5577:-501.976,-47.2617,0.0
+Chromosome	39158	.	C	G	2017.05	.	AB=0.0;AO=66;DP=66;QA=2297;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:66:0:0:66:2297:-206.967,-19.868,0.0
+Chromosome	42281	.	C	A	996.941	.	AB=0.0;AO=33;DP=33;QA=1179;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:33:0:0:33:1179:-106.407,-9.93399,0.0
+Chromosome	42967	.	G	C	2851.59	.	AB=0.0;AO=92;DP=92;QA=3244;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:92:0:0:92:3244:-292.146,-27.6948,0.0
+Chromosome	43347	.	T	C	2847.24	.	AB=0.0;AO=92;DP=92;QA=3233;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:92:0:0:92:3233:-291.161,-27.6948,0.0
+Chromosome	44768	.	A	G	3099.48	.	AB=0.0;AO=99;DP=99;QA=3501;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:99:0:0:99:3501:-315.241,-29.802,0.0
+Chromosome	49360	.	C	T	2971.13	.	AB=0.0;AO=97;DP=97;QA=3365;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:97:0:0:97:3365:-303.059,-29.1999,0.0
+Chromosome	49690	.	GCC	G	3479.85	.	AB=0.0;AO=117;DP=117;QA=3917;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:117:0:0:117:3917:-352.709,-35.2205,0.0
+Chromosome	50557	.	T	C	3743.4	.	AB=0.0;AO=121;DP=121;QA=4203;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:121:0:0:121:4203:-378.409,-36.4246,0.0
+Chromosome	51949	.	A	G	3521.52	.	AB=0.0;AO=112;DP=112;QA=3955;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:112:0:0:112:3955:-356.092,-33.7154,0.0
+Chromosome	54394	.	A	G	3304.32	.	AB=0.0;AO=104;DP=105;QA=3711;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:105:0:0:104:3711:-333.937,-31.3071,0.0
+Chromosome	62049	.	A	G	2249.46	.	AB=0.0;AO=77;DP=78;QA=2659;QR=35;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:78:1:35:77:2659:-236.018,-19.9817,0.0
+Chromosome	63146	.	G	T	5120.15	.	AB=0.0;AO=163;DP=163;QA=5737;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:163:0:0:163:5737:-516.376,-49.0679,0.0
+Chromosome	65150	.	C	T	4046.85	.	AB=0.0;AO=134;DP=134;QA=4538;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:134:0:0:134:4538:-408.565,-40.338,0.0
+Chromosome	65246	.	C	T	3297.8	.	AB=0.0;AO=106;DP=107;QA=3712;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:107:0:0:106:3712:-334.038,-31.9092,0.0
+Chromosome	68337	.	T	TC	1791.13	.	AB=0.0;AO=60;DP=61;QA=2038;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:61:0:0:60:2038:-183.378,-18.0618,0.0
+Chromosome	69989	.	G	A	3539.46	.	AB=0.0;AO=119;DP=119;QA=3973;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:119:0:0:119:3973:-357.725,-35.8226,0.0
+Chromosome	70267	.	G	T	3018.85	.	AB=0.0;AO=100;DP=101;QA=3421;QR=25;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:101:1:25:100:3421:-305.576,-27.9042,0.0
+Chromosome	70816	.	A	G	4198.57	.	AB=0.0;AO=136;DP=136;QA=4707;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:136:0:0:136:4707:-423.747,-40.9401,0.0
+Chromosome	71336	.	G	C	556.161	.	AB=0.0;AO=21;DP=21;QA=770;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:770:-69.6143,-6.32163,0.0
+Chromosome	71914	.	T	C	3905.06	.	AB=0.0;AO=126;DP=126;QA=4382;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:126:0:0:126:4382:-394.523,-37.9298,0.0
+Chromosome	75233	.	C	A	1903.61	.	AB=0.0;AO=64;DP=64;QA=2172;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:64:0:0:64:2172:-195.723,-19.2659,0.0
+Chromosome	75940	.	G	C	2674.83	.	AB=0.0;AO=89;DP=89;QA=3048;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:89:0:0:89:3048:-274.519,-26.7917,0.0
+Chromosome	87468	.	C	T	4061.4	.	AB=0.0;AO=126;DP=126;QA=4584;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:126:0:0:126:4584:-412.628,-37.9298,0.0
+Chromosome	92199	.	T	G	686.38	.	AB=0.0;AO=23;DP=23;QA=799;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:799:-72.2155,-6.92369,0.0
+Chromosome	94388	.	G	A	2922.87	.	AB=0.0;AO=95;DP=95;QA=3292;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:95:0:0:95:3292:-296.486,-28.5979,0.0
+Chromosome	99162	.	TCGGTGTGCG	T	2040.99	.	AB=0.0;AO=78;DP=78;QA=2358;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:78:0:0:78:2358:-212.453,-23.4803,0.0
+Chromosome	105139	.	C	A	3418.74	.	AB=0.0;AO=109;DP=110;QA=3888;QR=38;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:110:1:38:109:3888:-346.257,-29.316,0.0
+Chromosome	105736	.	T	C	1805.18	.	AB=0.0;AO=61;DP=61;QA=2101;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:61:0:0:61:2101:-189.335,-18.3628,0.0
+Chromosome	116000	.	T	G	3196.37	.	AB=0.0;AO=105;DP=105;QA=3605;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:105:0:0:105:3605:-324.628,-31.6082,0.0
+Chromosome	122109	.	A	G	3324.29	.	AB=0.0;AO=111;DP=111;QA=3735;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:111:0:0:111:3735:-336.329,-33.4143,0.0
+Chromosome	123454	.	C	T	4362.28	.	AB=0.0;AO=136;DP=137;QA=4894;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:137:0:0:136:4894:-440.321,-40.9401,0.0
+Chromosome	123520	.	T	C	3793.13	.	AB=0.0;AO=121;DP=121;QA=4262;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:121:0:0:121:4262:-383.682,-36.4246,0.0
+Chromosome	125711	.	GGTT	G	3140.7	.	AB=0.0;AO=105;DP=105;QA=3531;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:105:0:0:105:3531:-317.98,-31.6082,0.0
+Chromosome	125830	.	G	GA	2079.98	.	AB=0.0;AO=69;DP=72;QA=2347;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:72:0:0:69:2347:-211.164,-20.7711,0.0
+Chromosome	131174	.	T	TG	2854.04	.	AB=0.0;AO=97;DP=99;QA=3213;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:99:0:0:97:3213:-288.972,-29.1999,0.0
+Chromosome	133839	.	C	T	2457.55	.	AB=0.0;AO=78;DP=78;QA=2802;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:78:0:0:78:2802:-252.374,-23.4803,0.0
+Chromosome	134024	.	T	C	2242.53	.	AB=0.0;AO=72;DP=72;QA=2543;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:72:0:0:72:2543:-229.099,-21.6742,0.0
+Chromosome	138419	.	G	A	4166.36	.	AB=0.0;AO=132;DP=132;QA=4683;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:132:0:0:132:4683:-421.582,-39.736,0.0
+Chromosome	139297	.	G	T	3706.81	.	AB=0.0;AO=120;DP=120;QA=4165;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:120:0:0:120:4165:-374.978,-36.1236,0.0
+Chromosome	143207	.	T	C	2180.95	.	AB=0.0;AO=72;DP=72;QA=2523;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:72:0:0:72:2523:-227.3,-21.6742,0.0
+Chromosome	146087	.	T	C	4315.28	.	AB=0.0;AO=137;DP=137;QA=4844;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:137:0:0:137:4844:-436.07,-41.2411,0.0
+Chromosome	147262	.	G	T	3766.49	.	AB=0.0;AO=122;DP=122;QA=4228;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:122:0:0:122:4228:-380.649,-36.7257,0.0
+Chromosome	154283	.	T	C	4403.08	.	AB=0.0;AO=141;DP=141;QA=4941;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:141:0:0:141:4941:-444.791,-42.4452,0.0
+Chromosome	154990	.	G	T	4207.92	.	AB=0.0;AO=142;DP=143;QA=4724;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:143:0:0:142:4724:-424.969,-42.7463,0.0
+Chromosome	162151	.	GT	G	2208.67	.	AB=0.0;AO=81;DP=84;QA=2524;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:84:0:0:81:2524:-226.95,-24.3834,0.0
+Chromosome	163940	.	A	G	2507.97	.	AB=0.0;AO=80;DP=80;QA=2839;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:80:0:0:80:2839:-255.719,-24.0824,0.0
+Chromosome	166253	.	A	C	3141.13	.	AB=0.0;AO=102;DP=102;QA=3586;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:102:0:0:102:3586:-322.902,-30.7051,0.0
+Chromosome	177857	.	G	A	2984.02	.	AB=0.0;AO=98;DP=98;QA=3389;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:98:0:0:98:3389:-305.192,-29.5009,0.0
+Chromosome	188800	.	T	C	1887.67	.	AB=0.0;AO=64;DP=64;QA=2217;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:64:0:0:64:2217:-199.772,-19.2659,0.0
+Chromosome	190816	.	A	C	1715.49	.	AB=0.0;AO=57;DP=57;QA=2026;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:57:0:0:57:2026:-182.579,-17.1587,0.0
+Chromosome	194305	.	C	CGG	1602.78	.	AB=0.0;AO=58;DP=59;QA=1889;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:59:0:0:58:1889:-169.924,-17.4597,0.0
+Chromosome	3750185	.	CGAC	GGTG	1102.73	.	AB=0.0;AO=36;DP=36;QA=1255;QR=0;RO=0;TYPE=complex	GT:DP:RO:QR:AO:QA:GL	1/1:36:0:0:36:1255:-113.24,-10.8371,0.0
+Chromosome	3750193	.	G	A	1198.75	.	AB=0.0;AO=40;DP=40;QA=1367;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:40:0:0:40:1367:-123.307,-12.0412,0.0
diff -r 000000000000 -r 3b1e7c170b10 test-data/test_output4.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_output4.vcf	Thu Oct 10 17:59:02 2019 -0400
@@ -0,0 +1,58 @@
+##fileformat=VCFv4.1
+##fileDate=20150301
+##source=freeBayes v0.9.20-16-g3e35e72
+##reference=reference.fasta
+##phasing=none
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
+##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
+##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
+##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
+##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
+##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
+##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
+##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
+##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
+##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
+##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
+##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
+##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
+##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
+##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
+##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio.  Ratio between depth in samples with each called alternate allele and those without.">
+##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
+##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
+##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
+##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
+##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
+##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
+##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
+##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
+##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
+##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
+##INFO=<ID=technology.Illumina,Number=A,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from Illumina">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	BR_002	BR_004	BR_006	BR_009	BR_013	BR_015	BR_016	BR_021	BR_023	BR_024	BR_025	BR_028	BR_030	BR_031	BR_040	BR_041	BR_043	BR_046	BR_047	BR_048	WL_031	WL_032	WL_054	WL_056	WL_057	WL_058	WL_061	WL_064	WL_066	WL_067	WL_069	WL_070	WL_071	WL_072	WL_076	WL_077	WL_078	WL_079	WL_080	WL_081
+E2_L101	125	.	C	T	110675	.	AB=0.558397;ABP=37.7557;AC=47;AF=0.635135;AN=74;AO=1064;CIGAR=1X;DP=1923;DPB=1923.0;DPRA=0.800123;EPP=2313.46;EPPR=1866.13;GTI=0;LEN=1;MEANALT=1.02941;MQM=60.0;MQMR=60.0;NS=37;NUMALT=1;ODDS=7.31554;PAIRED=1.0;PAIREDR=1.0;PAO=0.0;PQA=0.0;PQR=0.0;PRO=0.0;QA=32732;QR=26625;RO=858;RPL=0.0;RPP=2313.46;RPPR=1866.13;RPR=1064.0;RUN=1;SAF=0;SAP=2313.46;SAR=1064;SRF=0;SRP=1866.13;SRR=858;TYPE=snp;technology.Illumina=1.0	GT:DP:RO:QR:AO:QA:GL	0/1:63:29:919:34:1086:-351.067,0.0,-296.04	0/1:275:136:3998:139:4075:-1396.19,0.0,-1365.26	0/1:17:7:231:10:323:-104.267,0.0,-71.9963	0/0:50:50:1463:0:0:0.0,-15.0515,-531.939	.:.:.:.:.:.:.	0/1:137:73:2205:64:1932:-644.905,0.0,-741.47	0/1:15:6:206:9:301:-94.9006,0.0,-62.3614	0/1:63:14:477:49:1547:-512.541,0.0,-136.291	0/1:5:3:93:2:69:-21.0475,0.0,-31.1725	1/1:13:0:0:13:388:-139.212,-3.91339,0.0	1/1:21:0:0:21:616:-223.722,-6.32163,0.0	0/1:32:7:224:25:787:-261.493,0.0,-66.8418	.:.:.:.:.:.:.	1/1:25:0:0:25:815:-273.654,-7.52575,0.0	0/1:45:23:652:22:616:-218.165,0.0,-229.408	1/1:39:0:0:39:1185:-418.932,-11.7402,0.0	0/1:49:16:469:33:949:-334.932,0.0,-155.746	0/0:14:14:396:0:0:0.0,-4.21442,-147.916	1/1:82:0:0:82:2334:-866.31,-24.6845,0.0	0/1:27:14:431:13:389:-131.174,0.0,-142.961	1/1:68:0:0:68:2019:-725.97,-20.47,0.0	1/1:16:0:0:16:493:-172.669,-4.81648,0.0	0/1:57:2:58:55:1716:-577.549,0.0,-4.35015	1/1:34:0:0:34:1117:-372.828,-10.235,0.0	0/1:25:9:295:16:540:-169.396,0.0,-91.3433	0/1:53:26:837:27:880:-279.548,0.0,-267.677	1/1:33:0:0:33:1063:-359.964,-9.93399,0.0	0/1:21:12:397:9:297:-92.7309,0.0,-125.728	0/1:107:50:1484:57:1738:-580.482,0.0,-501.622	1/1:9:0:0:9:282:-97.6869,-2.70927,0.0	1/1:22:0:0:22:711:-240.294,-6.62266,0.0	0/1:130:57:1814:72:2337:-747.579,0.0,-580.516	0/0:151:150:4800:1:31:0.0,-34.3561,-1621.09	1/1:26:0:0:26:813:-281.46,-7.82678,0.0	.:.:.:.:.:.:.	1/1:7:0:0:7:223:-76.3831,-2.10721,0.0	1/1:13:0:0:13:425:-142.565,-3.91339,0.0	0/0:127:127:4112:0:0:0.0,-38.2308,-1386.3	0/1:21:12:387:9:297:-92.7307,0.0,-124.822	0/1:31:21:677:10:338:-101.416,0.0,-219.904
+E2_L101	189	.	GT	GA	79493.6	.	AB=0.530648;ABP=12.3275;AC=27;AF=0.364865;AN=74;AO=711;CIGAR=1M1X;DP=1947;DPB=1947.0;DPRA=1.2223;EPP=1546.93;EPPR=2623.98;GTI=0;LEN=1;MEANALT=1.2;MQM=59.9536;MQMR=59.9528;NS=37;NUMALT=2;ODDS=8.57375;PAIRED=1.0;PAIREDR=1.0;PAO=0.0;PQA=0.0;PQR=0.0;PRO=0.0;QA=26768;QR=45917;RO=1207;RPL=711.0;RPP=1546.93;RPPR=2623.98;RPR=0.0;RUN=1;SAF=0;SAP=1546.93;SAR=711;SRF=0;SRP=2623.98;SRR=1207;TYPE=snp;technology.Illumina=1.0	GT:DP:RO:QR:AO:QA:GL	0/1:63:29:1128:33,0:1297,0:-362.019,0.0,-314.829,-370.749,-324.763,-695.435	0/1:279:136:5023:143,0:5199,0:-1527.93,0.0,-1456.1,-1568.87,-1499.14,-3067.65	0/0:18:18:720:0,0:0,0:0.0,-5.41854,-209.126,-5.41854,-209.126,-209.126	0/0:50:50:1802:0,0:0,0:0.0,-15.0515,-562.43,-15.0515,-562.43,-562.43	.:.:.:.:.:.:.	0/0:140:140:5188:0,0:0,0:0.0,-42.1442,-1586.93,-42.1442,-1586.93,-1586.93	0/0:15:15:612:0,0:0,0:0.0,-4.51545,-175.417,-4.51545,-175.417,-175.417	0/1:63:14:556:49,0:1902,0:-544.414,0.0,-143.417,-548.629,-158.168,-706.402	0/0:7:7:255:0,0:0,0:0.0,-2.10721,-79.294,-2.10721,-79.294,-79.294	1/1:13:0:0:13,0:486,0:-148.079,-3.91339,0.0,-148.079,-3.91339,-148.079	0/1:21:10:377:11,0:413,0:-119.194,0.0,-107.957,-122.204,-111.268,-233.097	0/1:33:7:283:26,0:969,0:-285.557,0.0,-71.9094,-287.664,-79.7362,-367.003	.:.:.:.:.:.:.	0/1:26:19:720:7,0:270,0:-72.8033,0.0,-209.291,-78.5229,-211.398,-289.538	0/0:45:45:1610:0,0:0,0:0.0,-13.5463,-505.167,-13.5463,-505.167,-505.167	1/2:39:0:0:17,22:633,823:-431.573,-243.764,-238.646,-188.182,0.0,-181.559	0/1:49:16:571:33,0:1209,0:-358.342,0.0,-164.964,-363.158,-174.898,-537.697	0/0:14:14:515:0,0:0,0:0.0,-4.21442,-158.684,-4.21442,-158.684,-158.684	0/1:82:37:1340:45,0:1616,0:-481.016,0.0,-392.198,-492.154,-405.744,-897.538	0/1:27:14:522:13,0:489,0:-140.222,0.0,-151.186,-144.436,-155.1,-299.162	1/1:69:0:0:69,0:2506,0:-777.734,-20.7711,0.0,-777.734,-20.7711,-777.734	0/1:17:10:355:7,0:270,0:-75.5457,0.0,-107.162,-78.556,-109.269,-187.452	0/1:58:33:1252:25,0:989,0:-271.846,0.0,-359.488,-281.78,-367.013,-648.405	0/1:35:19:755:16,0:627,0:-174.228,0.0,-209.735,-179.947,-214.551,-394.104	0/1:26:9:351:17,0:680,0:-189.701,0.0,-96.1193,-192.41,-101.237,-293.254	0/0:53:53:2059:0,0:0,0:0.0,-15.9546,-609.511,-15.9546,-609.511,-609.511	0/0:33:32:1269:0,0:0,0:0.0,-9.63296,-370.162,-9.63296,-370.162,-370.162	0/1:21:12:477:9,0:365,0:-98.8929,0.0,-132.958,-102.505,-135.668,-237.771	0/1:107:52:1896:55,0:2071,0:-594.399,0.0,-554.667,-610.053,-571.224,-1180.91	0/1:9:7:281:2,0:50,0:-18.0366,0.0,-78.9529,-20.1438,-79.555,-99.4154	1/1:22:0:0:22,0:864,0:-254.067,-6.62266,0.0,-254.067,-6.62266,-254.067	0/1:131:57:2263:72,0:2808,0:-789.722,0.0,-620.658,-806.881,-642.332,-1449.1	0/0:152:150:5887:1,0:38,0:0.0,-34.038,-1717.85,-45.1545,-1718.15,-1729.26	0/1:27:14:534:13,0:512,0:-142.297,0.0,-152.267,-146.511,-156.181,-302.304	.:.:.:.:.:.:.	0/1:7:3:113:4,0:158,0:-44.4921,0.0,-32.4297,-45.3952,-33.6338,-78.6449	0/0:14:14:544:0,0:0,0:0.0,-4.21442,-161.298,-4.21442,-161.298,-161.298	0/0:129:127:4963:0,0:0,0:0.0,-38.2308,-1462.3,-38.2308,-1462.3,-1462.3	0/1:22:13:480:9,0:347,0:-96.9577,0.0,-140.907,-100.871,-143.616,-244.109	0/0:31:31:1216:0,0:0,0:0.0,-9.33193,-357.713,-9.33193,-357.713,-357.713
diff -r 000000000000 -r 3b1e7c170b10 test-data/test_output5.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_output5.vcf	Thu Oct 10 17:59:02 2019 -0400
@@ -0,0 +1,98 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20190323
+##source=freeBayes v1.2.0-dirty
+##reference=reference/ref.fa
+##contig=<ID=Chromosome,length=4411532>
+##phasing=none
+##commandline="freebayes -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam --region Chromosome:0-1495044"
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
+##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
+##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
+##bcftools_viewVersion=1.9+htslib-1.9
+##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=100.0 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Sat Mar 23 06:45:26 2019
+##bcftools_annotateVersion=1.9+htslib-1.9
+##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Sat Mar 23 06:45:26 2019
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	out
+Chromosome	1849	.	C	A	3412.24	.	AB=0.0;AO=110;DP=110;QA=3850;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:110:0:0:110:3850:-346.644,-33.1133,0.0
+Chromosome	1977	.	A	G	3234.43	.	AB=0.0;AO=106;DP=106;QA=3704;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:106:0:0:106:3704:-333.508,-31.9092,0.0
+Chromosome	4013	.	T	C	3965.91	.	AB=0.0;AO=125;DP=125;QA=4448;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:125:0:0:125:4448:-400.411,-37.6288,0.0
+Chromosome	7362	.	G	C	4009.71	.	AB=0.0;AO=126;DP=126;QA=4518;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:126:0:0:126:4518:-406.711,-37.9298,0.0
+Chromosome	9304	.	G	A	4222.23	.	AB=0.0;AO=136;DP=136;QA=4764;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:136:0:0:136:4764:-428.865,-40.9401,0.0
+Chromosome	11820	.	C	G	2252.54	.	AB=0.0;AO=74;DP=74;QA=2662;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:74:0:0:74:2662:-239.791,-22.2762,0.0
+Chromosome	11879	.	A	G	1815.99	.	AB=0.0;AO=63;DP=63;QA=2212;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:63:0:0:63:2212:-199.306,-18.9649,0.0
+Chromosome	14785	.	T	C	4342.4	.	AB=0.0;AO=139;DP=139;QA=4874;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:139:0:0:139:4874:-438.763,-41.8432,0.0
+Chromosome	14861	.	G	T	4237.79	.	AB=0.0;AO=133;DP=135;QA=4758;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:135:0:0:133:4758:-427.969,-40.037,0.0
+Chromosome	15117	.	C	G	3298.26	.	AB=0.0;AO=106;DP=106;QA=3708;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:106:0:0:106:3708:-333.903,-31.9092,0.0
+Chromosome	15890	.	G	A	3349.13	.	AB=0.0;AO=116;DP=117;QA=3770;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:117:0:0:116:3770:-339.321,-34.9195,0.0
+Chromosome	16119	.	C	A	3794.09	.	AB=0.0;AO=124;DP=125;QA=4268;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:125:0:0:124:4268:-383.905,-37.3277,0.0
+Chromosome	25610	.	G	C	2779.82	.	AB=0.0;AO=89;DP=89;QA=3137;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:89:0:0:89:3137:-282.515,-26.7917,0.0
+Chromosome	26959	.	C	G	2791.1	.	AB=0.0;AO=91;DP=91;QA=3152;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:91:0:0:91:3152:-283.856,-27.3937,0.0
+Chromosome	27455	.	T	C	1646.76	.	AB=0.0;AO=52;DP=52;QA=1868;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:52:0:0:52:1868:-168.374,-15.6536,0.0
+Chromosome	28366	.	AT	A	2447.14	.	AB=0.0;AO=82;DP=84;QA=2764;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:84:0:0:82:2764:-248.651,-24.6845,0.0
+Chromosome	34044	.	T	C	3866.76	.	AB=0.0;AO=122;DP=122;QA=4351;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:122:0:0:122:4351:-391.712,-36.7257,0.0
+Chromosome	36008	.	G	C	2942.73	.	AB=0.0;AO=98;DP=101;QA=3356;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:101:0:0:98:3356:-301.935,-29.5009,0.0
+Chromosome	37031	.	C	G	3922.6	.	AB=0.0;AO=128;DP=129;QA=4437;QR=34;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:129:1:34:128:4437:-396.072,-35.434,0.0
+Chromosome	37305	.	C	G	4975.87	.	AB=0.0;AO=157;DP=157;QA=5577;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:157:0:0:157:5577:-501.976,-47.2617,0.0
+Chromosome	39158	.	C	G	2017.05	.	AB=0.0;AO=66;DP=66;QA=2297;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:66:0:0:66:2297:-206.967,-19.868,0.0
+Chromosome	42281	.	C	A	996.941	.	AB=0.0;AO=33;DP=33;QA=1179;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:33:0:0:33:1179:-106.407,-9.93399,0.0
+Chromosome	42967	.	G	C	2851.59	.	AB=0.0;AO=92;DP=92;QA=3244;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:92:0:0:92:3244:-292.146,-27.6948,0.0
+Chromosome	43347	.	T	C	2847.24	.	AB=0.0;AO=92;DP=92;QA=3233;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:92:0:0:92:3233:-291.161,-27.6948,0.0
+Chromosome	44768	.	A	G	3099.48	.	AB=0.0;AO=99;DP=99;QA=3501;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:99:0:0:99:3501:-315.241,-29.802,0.0
+Chromosome	49360	.	C	T	2971.13	.	AB=0.0;AO=97;DP=97;QA=3365;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:97:0:0:97:3365:-303.059,-29.1999,0.0
+Chromosome	49690	.	GCC	G	3479.85	.	AB=0.0;AO=117;DP=117;QA=3917;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:117:0:0:117:3917:-352.709,-35.2205,0.0
+Chromosome	50557	.	T	C	3743.4	.	AB=0.0;AO=121;DP=121;QA=4203;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:121:0:0:121:4203:-378.409,-36.4246,0.0
+Chromosome	51949	.	A	G	3521.52	.	AB=0.0;AO=112;DP=112;QA=3955;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:112:0:0:112:3955:-356.092,-33.7154,0.0
+Chromosome	54394	.	A	G	3304.32	.	AB=0.0;AO=104;DP=105;QA=3711;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:105:0:0:104:3711:-333.937,-31.3071,0.0
+Chromosome	62049	.	A	G	2249.46	.	AB=0.0;AO=77;DP=78;QA=2659;QR=35;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:78:1:35:77:2659:-236.018,-19.9817,0.0
+Chromosome	63146	.	G	T	5120.15	.	AB=0.0;AO=163;DP=163;QA=5737;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:163:0:0:163:5737:-516.376,-49.0679,0.0
+Chromosome	65150	.	C	T	4046.85	.	AB=0.0;AO=134;DP=134;QA=4538;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:134:0:0:134:4538:-408.565,-40.338,0.0
+Chromosome	65246	.	C	T	3297.8	.	AB=0.0;AO=106;DP=107;QA=3712;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:107:0:0:106:3712:-334.038,-31.9092,0.0
+Chromosome	68337	.	T	TC	1791.13	.	AB=0.0;AO=60;DP=61;QA=2038;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:61:0:0:60:2038:-183.378,-18.0618,0.0
+Chromosome	69989	.	G	A	3539.46	.	AB=0.0;AO=119;DP=119;QA=3973;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:119:0:0:119:3973:-357.725,-35.8226,0.0
+Chromosome	70267	.	G	T	3018.85	.	AB=0.0;AO=100;DP=101;QA=3421;QR=25;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:101:1:25:100:3421:-305.576,-27.9042,0.0
+Chromosome	70816	.	A	G	4198.57	.	AB=0.0;AO=136;DP=136;QA=4707;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:136:0:0:136:4707:-423.747,-40.9401,0.0
+Chromosome	71914	.	T	C	3905.06	.	AB=0.0;AO=126;DP=126;QA=4382;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:126:0:0:126:4382:-394.523,-37.9298,0.0
+Chromosome	75233	.	C	A	1903.61	.	AB=0.0;AO=64;DP=64;QA=2172;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:64:0:0:64:2172:-195.723,-19.2659,0.0
+Chromosome	75940	.	G	C	2674.83	.	AB=0.0;AO=89;DP=89;QA=3048;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:89:0:0:89:3048:-274.519,-26.7917,0.0
+Chromosome	87468	.	C	T	4061.4	.	AB=0.0;AO=126;DP=126;QA=4584;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:126:0:0:126:4584:-412.628,-37.9298,0.0
+Chromosome	94388	.	G	A	2922.87	.	AB=0.0;AO=95;DP=95;QA=3292;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:95:0:0:95:3292:-296.486,-28.5979,0.0
+Chromosome	99162	.	TCGGTGTGCG	T	2040.99	.	AB=0.0;AO=78;DP=78;QA=2358;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:78:0:0:78:2358:-212.453,-23.4803,0.0
+Chromosome	105139	.	C	A	3418.74	.	AB=0.0;AO=109;DP=110;QA=3888;QR=38;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:110:1:38:109:3888:-346.257,-29.316,0.0
+Chromosome	105736	.	T	C	1805.18	.	AB=0.0;AO=61;DP=61;QA=2101;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:61:0:0:61:2101:-189.335,-18.3628,0.0
+Chromosome	116000	.	T	G	3196.37	.	AB=0.0;AO=105;DP=105;QA=3605;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:105:0:0:105:3605:-324.628,-31.6082,0.0
+Chromosome	122109	.	A	G	3324.29	.	AB=0.0;AO=111;DP=111;QA=3735;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:111:0:0:111:3735:-336.329,-33.4143,0.0
+Chromosome	123454	.	C	T	4362.28	.	AB=0.0;AO=136;DP=137;QA=4894;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:137:0:0:136:4894:-440.321,-40.9401,0.0
+Chromosome	123520	.	T	C	3793.13	.	AB=0.0;AO=121;DP=121;QA=4262;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:121:0:0:121:4262:-383.682,-36.4246,0.0
+Chromosome	125711	.	GGTT	G	3140.7	.	AB=0.0;AO=105;DP=105;QA=3531;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:105:0:0:105:3531:-317.98,-31.6082,0.0
+Chromosome	125830	.	G	GA	2079.98	.	AB=0.0;AO=69;DP=72;QA=2347;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:72:0:0:69:2347:-211.164,-20.7711,0.0
+Chromosome	131174	.	T	TG	2854.04	.	AB=0.0;AO=97;DP=99;QA=3213;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:99:0:0:97:3213:-288.972,-29.1999,0.0
+Chromosome	133839	.	C	T	2457.55	.	AB=0.0;AO=78;DP=78;QA=2802;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:78:0:0:78:2802:-252.374,-23.4803,0.0
+Chromosome	134024	.	T	C	2242.53	.	AB=0.0;AO=72;DP=72;QA=2543;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:72:0:0:72:2543:-229.099,-21.6742,0.0
+Chromosome	138419	.	G	A	4166.36	.	AB=0.0;AO=132;DP=132;QA=4683;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:132:0:0:132:4683:-421.582,-39.736,0.0
+Chromosome	139297	.	G	T	3706.81	.	AB=0.0;AO=120;DP=120;QA=4165;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:120:0:0:120:4165:-374.978,-36.1236,0.0
+Chromosome	143207	.	T	C	2180.95	.	AB=0.0;AO=72;DP=72;QA=2523;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:72:0:0:72:2523:-227.3,-21.6742,0.0
+Chromosome	146087	.	T	C	4315.28	.	AB=0.0;AO=137;DP=137;QA=4844;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:137:0:0:137:4844:-436.07,-41.2411,0.0
+Chromosome	147262	.	G	T	3766.49	.	AB=0.0;AO=122;DP=122;QA=4228;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:122:0:0:122:4228:-380.649,-36.7257,0.0
+Chromosome	154283	.	T	C	4403.08	.	AB=0.0;AO=141;DP=141;QA=4941;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:141:0:0:141:4941:-444.791,-42.4452,0.0
+Chromosome	154990	.	G	T	4207.92	.	AB=0.0;AO=142;DP=143;QA=4724;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:143:0:0:142:4724:-424.969,-42.7463,0.0
+Chromosome	162151	.	GT	G	2208.67	.	AB=0.0;AO=81;DP=84;QA=2524;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:84:0:0:81:2524:-226.95,-24.3834,0.0
+Chromosome	163940	.	A	G	2507.97	.	AB=0.0;AO=80;DP=80;QA=2839;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:80:0:0:80:2839:-255.719,-24.0824,0.0
+Chromosome	166253	.	A	C	3141.13	.	AB=0.0;AO=102;DP=102;QA=3586;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:102:0:0:102:3586:-322.902,-30.7051,0.0
+Chromosome	177857	.	G	A	2984.02	.	AB=0.0;AO=98;DP=98;QA=3389;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:98:0:0:98:3389:-305.192,-29.5009,0.0
+Chromosome	188800	.	T	C	1887.67	.	AB=0.0;AO=64;DP=64;QA=2217;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:64:0:0:64:2217:-199.772,-19.2659,0.0
+Chromosome	190816	.	A	C	1715.49	.	AB=0.0;AO=57;DP=57;QA=2026;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:57:0:0:57:2026:-182.579,-17.1587,0.0
+Chromosome	194305	.	C	CGG	1602.78	.	AB=0.0;AO=58;DP=59;QA=1889;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:59:0:0:58:1889:-169.924,-17.4597,0.0
+Chromosome	3750185	.	CGAC	GGTG	1102.73	.	AB=0.0;AO=36;DP=36;QA=1255;QR=0;RO=0;TYPE=complex	GT:DP:RO:QR:AO:QA:GL	1/1:36:0:0:36:1255:-113.24,-10.8371,0.0
+Chromosome	3750193	.	G	A	1198.75	.	AB=0.0;AO=40;DP=40;QA=1367;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:40:0:0:40:1367:-123.307,-12.0412,0.0
diff -r 000000000000 -r 3b1e7c170b10 test-data/test_output6.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_output6.vcf	Thu Oct 10 17:59:02 2019 -0400
@@ -0,0 +1,92 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20190323
+##source=freeBayes v1.2.0-dirty
+##reference=reference/ref.fa
+##contig=<ID=Chromosome,length=4411532>
+##phasing=none
+##commandline="freebayes -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam --region Chromosome:0-1495044"
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
+##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
+##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
+##bcftools_viewVersion=1.9+htslib-1.9
+##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=100.0 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Sat Mar 23 06:45:26 2019
+##bcftools_annotateVersion=1.9+htslib-1.9
+##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Sat Mar 23 06:45:26 2019
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	out
+Chromosome	1849	.	C	A	3412.24	.	AB=0.0;AO=110;DP=110;QA=3850;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:110:0:0:110:3850:-346.644,-33.1133,0.0
+Chromosome	1977	.	A	G	3234.43	.	AB=0.0;AO=106;DP=106;QA=3704;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:106:0:0:106:3704:-333.508,-31.9092,0.0
+Chromosome	4013	.	T	C	3965.91	.	AB=0.0;AO=125;DP=125;QA=4448;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:125:0:0:125:4448:-400.411,-37.6288,0.0
+Chromosome	7362	.	G	C	4009.71	.	AB=0.0;AO=126;DP=126;QA=4518;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:126:0:0:126:4518:-406.711,-37.9298,0.0
+Chromosome	9304	.	G	A	4222.23	.	AB=0.0;AO=136;DP=136;QA=4764;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:136:0:0:136:4764:-428.865,-40.9401,0.0
+Chromosome	11820	.	C	G	2252.54	.	AB=0.0;AO=74;DP=74;QA=2662;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:74:0:0:74:2662:-239.791,-22.2762,0.0
+Chromosome	11879	.	A	G	1815.99	.	AB=0.0;AO=63;DP=63;QA=2212;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:63:0:0:63:2212:-199.306,-18.9649,0.0
+Chromosome	14785	.	T	C	4342.4	.	AB=0.0;AO=139;DP=139;QA=4874;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:139:0:0:139:4874:-438.763,-41.8432,0.0
+Chromosome	14861	.	G	T	4237.79	.	AB=0.0;AO=133;DP=135;QA=4758;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:135:0:0:133:4758:-427.969,-40.037,0.0
+Chromosome	15117	.	C	G	3298.26	.	AB=0.0;AO=106;DP=106;QA=3708;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:106:0:0:106:3708:-333.903,-31.9092,0.0
+Chromosome	15890	.	G	A	3349.13	.	AB=0.0;AO=116;DP=117;QA=3770;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:117:0:0:116:3770:-339.321,-34.9195,0.0
+Chromosome	16119	.	C	A	3794.09	.	AB=0.0;AO=124;DP=125;QA=4268;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:125:0:0:124:4268:-383.905,-37.3277,0.0
+Chromosome	21795	.	G	A	768.571	.	AB=0.0;AO=28;DP=28;QA=892;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:892:-80.5646,-8.42884,0.0
+Chromosome	25610	.	G	C	2779.82	.	AB=0.0;AO=89;DP=89;QA=3137;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:89:0:0:89:3137:-282.515,-26.7917,0.0
+Chromosome	26959	.	C	G	2791.1	.	AB=0.0;AO=91;DP=91;QA=3152;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:91:0:0:91:3152:-283.856,-27.3937,0.0
+Chromosome	27455	.	T	C	1646.76	.	AB=0.0;AO=52;DP=52;QA=1868;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:52:0:0:52:1868:-168.374,-15.6536,0.0
+Chromosome	34044	.	T	C	3866.76	.	AB=0.0;AO=122;DP=122;QA=4351;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:122:0:0:122:4351:-391.712,-36.7257,0.0
+Chromosome	36008	.	G	C	2942.73	.	AB=0.0;AO=98;DP=101;QA=3356;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:101:0:0:98:3356:-301.935,-29.5009,0.0
+Chromosome	37031	.	C	G	3922.6	.	AB=0.0;AO=128;DP=129;QA=4437;QR=34;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:129:1:34:128:4437:-396.072,-35.434,0.0
+Chromosome	37305	.	C	G	4975.87	.	AB=0.0;AO=157;DP=157;QA=5577;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:157:0:0:157:5577:-501.976,-47.2617,0.0
+Chromosome	39158	.	C	G	2017.05	.	AB=0.0;AO=66;DP=66;QA=2297;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:66:0:0:66:2297:-206.967,-19.868,0.0
+Chromosome	42281	.	C	A	996.941	.	AB=0.0;AO=33;DP=33;QA=1179;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:33:0:0:33:1179:-106.407,-9.93399,0.0
+Chromosome	42967	.	G	C	2851.59	.	AB=0.0;AO=92;DP=92;QA=3244;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:92:0:0:92:3244:-292.146,-27.6948,0.0
+Chromosome	43347	.	T	C	2847.24	.	AB=0.0;AO=92;DP=92;QA=3233;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:92:0:0:92:3233:-291.161,-27.6948,0.0
+Chromosome	44768	.	A	G	3099.48	.	AB=0.0;AO=99;DP=99;QA=3501;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:99:0:0:99:3501:-315.241,-29.802,0.0
+Chromosome	49360	.	C	T	2971.13	.	AB=0.0;AO=97;DP=97;QA=3365;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:97:0:0:97:3365:-303.059,-29.1999,0.0
+Chromosome	50557	.	T	C	3743.4	.	AB=0.0;AO=121;DP=121;QA=4203;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:121:0:0:121:4203:-378.409,-36.4246,0.0
+Chromosome	51949	.	A	G	3521.52	.	AB=0.0;AO=112;DP=112;QA=3955;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:112:0:0:112:3955:-356.092,-33.7154,0.0
+Chromosome	54394	.	A	G	3304.32	.	AB=0.0;AO=104;DP=105;QA=3711;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:105:0:0:104:3711:-333.937,-31.3071,0.0
+Chromosome	62049	.	A	G	2249.46	.	AB=0.0;AO=77;DP=78;QA=2659;QR=35;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:78:1:35:77:2659:-236.018,-19.9817,0.0
+Chromosome	63146	.	G	T	5120.15	.	AB=0.0;AO=163;DP=163;QA=5737;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:163:0:0:163:5737:-516.376,-49.0679,0.0
+Chromosome	65150	.	C	T	4046.85	.	AB=0.0;AO=134;DP=134;QA=4538;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:134:0:0:134:4538:-408.565,-40.338,0.0
+Chromosome	65246	.	C	T	3297.8	.	AB=0.0;AO=106;DP=107;QA=3712;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:107:0:0:106:3712:-334.038,-31.9092,0.0
+Chromosome	69989	.	G	A	3539.46	.	AB=0.0;AO=119;DP=119;QA=3973;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:119:0:0:119:3973:-357.725,-35.8226,0.0
+Chromosome	70267	.	G	T	3018.85	.	AB=0.0;AO=100;DP=101;QA=3421;QR=25;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:101:1:25:100:3421:-305.576,-27.9042,0.0
+Chromosome	70816	.	A	G	4198.57	.	AB=0.0;AO=136;DP=136;QA=4707;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:136:0:0:136:4707:-423.747,-40.9401,0.0
+Chromosome	71336	.	G	C	556.161	.	AB=0.0;AO=21;DP=21;QA=770;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:770:-69.6143,-6.32163,0.0
+Chromosome	71914	.	T	C	3905.06	.	AB=0.0;AO=126;DP=126;QA=4382;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:126:0:0:126:4382:-394.523,-37.9298,0.0
+Chromosome	75233	.	C	A	1903.61	.	AB=0.0;AO=64;DP=64;QA=2172;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:64:0:0:64:2172:-195.723,-19.2659,0.0
+Chromosome	75940	.	G	C	2674.83	.	AB=0.0;AO=89;DP=89;QA=3048;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:89:0:0:89:3048:-274.519,-26.7917,0.0
+Chromosome	87468	.	C	T	4061.4	.	AB=0.0;AO=126;DP=126;QA=4584;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:126:0:0:126:4584:-412.628,-37.9298,0.0
+Chromosome	92199	.	T	G	686.38	.	AB=0.0;AO=23;DP=23;QA=799;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:799:-72.2155,-6.92369,0.0
+Chromosome	94388	.	G	A	2922.87	.	AB=0.0;AO=95;DP=95;QA=3292;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:95:0:0:95:3292:-296.486,-28.5979,0.0
+Chromosome	105139	.	C	A	3418.74	.	AB=0.0;AO=109;DP=110;QA=3888;QR=38;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:110:1:38:109:3888:-346.257,-29.316,0.0
+Chromosome	105736	.	T	C	1805.18	.	AB=0.0;AO=61;DP=61;QA=2101;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:61:0:0:61:2101:-189.335,-18.3628,0.0
+Chromosome	116000	.	T	G	3196.37	.	AB=0.0;AO=105;DP=105;QA=3605;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:105:0:0:105:3605:-324.628,-31.6082,0.0
+Chromosome	122109	.	A	G	3324.29	.	AB=0.0;AO=111;DP=111;QA=3735;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:111:0:0:111:3735:-336.329,-33.4143,0.0
+Chromosome	123454	.	C	T	4362.28	.	AB=0.0;AO=136;DP=137;QA=4894;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:137:0:0:136:4894:-440.321,-40.9401,0.0
+Chromosome	123520	.	T	C	3793.13	.	AB=0.0;AO=121;DP=121;QA=4262;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:121:0:0:121:4262:-383.682,-36.4246,0.0
+Chromosome	133839	.	C	T	2457.55	.	AB=0.0;AO=78;DP=78;QA=2802;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:78:0:0:78:2802:-252.374,-23.4803,0.0
+Chromosome	134024	.	T	C	2242.53	.	AB=0.0;AO=72;DP=72;QA=2543;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:72:0:0:72:2543:-229.099,-21.6742,0.0
+Chromosome	138419	.	G	A	4166.36	.	AB=0.0;AO=132;DP=132;QA=4683;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:132:0:0:132:4683:-421.582,-39.736,0.0
+Chromosome	139297	.	G	T	3706.81	.	AB=0.0;AO=120;DP=120;QA=4165;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:120:0:0:120:4165:-374.978,-36.1236,0.0
+Chromosome	143207	.	T	C	2180.95	.	AB=0.0;AO=72;DP=72;QA=2523;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:72:0:0:72:2523:-227.3,-21.6742,0.0
+Chromosome	146087	.	T	C	4315.28	.	AB=0.0;AO=137;DP=137;QA=4844;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:137:0:0:137:4844:-436.07,-41.2411,0.0
+Chromosome	147262	.	G	T	3766.49	.	AB=0.0;AO=122;DP=122;QA=4228;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:122:0:0:122:4228:-380.649,-36.7257,0.0
+Chromosome	154283	.	T	C	4403.08	.	AB=0.0;AO=141;DP=141;QA=4941;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:141:0:0:141:4941:-444.791,-42.4452,0.0
+Chromosome	154990	.	G	T	4207.92	.	AB=0.0;AO=142;DP=143;QA=4724;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:143:0:0:142:4724:-424.969,-42.7463,0.0
+Chromosome	163940	.	A	G	2507.97	.	AB=0.0;AO=80;DP=80;QA=2839;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:80:0:0:80:2839:-255.719,-24.0824,0.0
+Chromosome	166253	.	A	C	3141.13	.	AB=0.0;AO=102;DP=102;QA=3586;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:102:0:0:102:3586:-322.902,-30.7051,0.0
+Chromosome	177857	.	G	A	2984.02	.	AB=0.0;AO=98;DP=98;QA=3389;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:98:0:0:98:3389:-305.192,-29.5009,0.0
+Chromosome	188800	.	T	C	1887.67	.	AB=0.0;AO=64;DP=64;QA=2217;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:64:0:0:64:2217:-199.772,-19.2659,0.0
+Chromosome	190816	.	A	C	1715.49	.	AB=0.0;AO=57;DP=57;QA=2026;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:57:0:0:57:2026:-182.579,-17.1587,0.0
+Chromosome	2738274	.	A	C	511.15	.	AB=0.0;AO=18;DP=19;QA=633;QR=35;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:19:1:35:18:633:-53.7923,-2.22094,0.0
+Chromosome	3750193	.	G	A	1198.75	.	AB=0.0;AO=40;DP=40;QA=1367;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:40:0:0:40:1367:-123.307,-12.0412,0.0