# HG changeset patch
# User iuc
# Date 1574102747 18000
# Node ID fd2d6e035c3f3d734857c5cb7c4e280a38483953
# Parent  f41a1e03538baf1b58a69d21fd669b47fa31ea59
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"

diff -r f41a1e03538b -r fd2d6e035c3f gatk4_Mutect2.xml
--- a/gatk4_Mutect2.xml	Wed Oct 30 15:33:59 2019 -0400
+++ b/gatk4_Mutect2.xml	Mon Nov 18 13:45:47 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@WRAPPER_VERSION@0" profile="18.05">
+<tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@WRAPPER_VERSION@1" profile="18.05">
     <description>- Call somatic SNVs and indels via local assembly of haplotypes</description>
     <macros>
         <import>macros.xml</import>
@@ -62,16 +62,6 @@
                 #end if
             #end if
 
-            #if $optional.population_callset
-                #set datatype = $optional.population_callset.datatype
-                #if $optional.population_callset.is_of_type("vcf_bgzip")
-                    ln -s '$optional.population_callset' population_callset.vcf.gz &&
-                    tabix population_callset.vcf.gz &&
-                #else
-                    ln -s '$optional.population_callset' population_callset.vcf &&
-                #end if
-            #end if
-
             #if $optional.alleles
                 #set datatype = $optional.alleles.datatype
                 #if $optional.alleles.is_of_type("vcf_bgzip")
@@ -90,34 +80,6 @@
 
         #include source=$gatk_bam_input#
 
-        ## COMMON PARAMETERS ##
-
-        #if str($common.common_parameters) == 'yes'
-
-            #if $common.read_filter
-                #for $filter in str($common.read_filter).split(',')
-                    --read-filter="$filter"
-                #end for
-            #end if
-
-            #if $common.disable_read_filter
-                #for $filter in str($common.disable_read_filter).split(',')
-                    --disable-read-filter="$filter"
-                #end for
-            #end if
-
-            --verbosity="ERROR"
-            --read-validation-stringency="$common.read_validation_stringency"
-            --interval-set-rule="$common.interval_set_rule"
-            $common.lenient
-            $common.disable_tool_default_read_filters
-            $common.add_output_sam_program_record
-            $common.add_output_vcf_command_line
-
-        #end if
-
-        ## END COMMON PARAMETERS ##
-
         ## OPTIONAL PARAMETERS ##
 
         #if str($optional.optional_parameters) == 'yes'
@@ -172,26 +134,71 @@
                 --alleles alleles.vcf
             #end if
 
+            #if $optional.f1r2_max_depth:
+                --f1r2-max-depth="$optional.f1r2_max_depth"
+            #end if
+
+            #if $optional.f1r2_max_depth:
+                --f1r2-median-mq="$optional.f1r2_median_mq"
+            #end if
+
+            #if $optional.f1r2_max_depth:
+                --f1r2-min-bq="$optional.f1r2_min_bq"
+            #end if
+
+            #if $optional.interval_merging_rule:
+                --interval-merging-rule="$optional.interval_merging_rule"
+            #end if
+
+            #if $optional.interval_set_rule:
+                --interval-set-rule="$optional.interval_set_rule"
+            #end if
+
+            #if $optional.pcr_indel_qual:
+                --pcr-indel-qual="$optional.pcr_indel_qual"
+            #end if
+
+            #if $optional.pcr_snv_qual:
+                --pcr-snv-qual="$optional.pcr_snv_qual"
+            #end if
+
+            #if $optional.read_filter
+                #for $filter in str($optional.read_filter).split(',')
+                    --read-filter="$filter"
+                #end for
+            #end if
+
+            #if $optional.disable_read_filter
+                #for $filter in str($optional.disable_read_filter).split(',')
+                    --disable-read-filter="$filter"
+                #end for
+            #end if
+
             --base-quality-score-threshold="$optional.base_quality_score_threshold"
             --af-of-alleles-not-in-resource="$optional.af_of_alleles_not_in_resource"
             --downsampling-stride="$optional.downsampling_stride"
             --gcs-max-retries="$optional.gcs_max_retries"
             --initial-tumor-lod="$optional.initial_tumor_lod"
-            --interval-merging-rule="$optional.interval_merging_rule"
             --max-population-af="$optional.max_population_af"
             --max-reads-per-alignment-start="$optional.max_reads_per_alignment_start"
             --min-base-quality-score="$optional.min_base_quality_score"
             --native-pair-hmm-threads="\${GALAXY_SLOTS:-1}"
             --normal-lod="$optional.normal_lod"
+            --read-validation-stringency="$optional.read_validation_stringency"
             --tumor-lod-to-emit="$optional.tumor_lod_to_emit"
+            --verbosity="ERROR"
+            $optional.lenient
             $optional.annotate_with_num_discovered_alleles
+            $optional.add_output_sam_program_record
             $optional.disable_bam_index_caching
             $optional.disable_sequence_dictionary_validation
             $optional.genotype_germline_sites
             $optional.genotype_pon_sites
+            $optional.ignore_itr_artifacts
+            $optional.mitochondria_mode
             $optional.native_pair_hmm_use_double_precision
             $optional.sites_only_vcf_output
-            $optional.use_new_qual_calculator
+            $optional.add_output_vcf_command_line
         #end if
 
         ## END OPTIONAL PARAMETERS ##
@@ -200,12 +207,20 @@
 
         #if str($advanced.advanced_parameters) == 'yes'
 
-            #if $advanced.input_prior
-                --input-prior="$advanced.input_prior"
+            #if $advanced.kmer_size
+                --kmer-size="$advanced.kmer_size"
             #end if
 
-            #if $advanced.kmer_size
-                --kmer-size="$advanced.kmer_size"
+            #if $advanced.gvcf_lod_band
+                --gvcf-lod-band="$advanced.gvcf_lod_band"
+            #end if
+
+            #if $advanced.emit_ref_confidence
+                --emit-ref-confidence="$advanced.emit_ref_confidence"
+            #end if
+
+            #if $advanced.max_unpruned_variants
+                --max-unpruned-variants="$advanced.max_unpruned_variants"
             #end if
 
             --active-probability-threshold="$advanced.active_probability_threshold"
@@ -219,22 +234,26 @@
             --min-assembly-region-size="$advanced.min_assembly_region_size"
             --min-dangling-branch-length="$advanced.min_dangling_branch_length"
             --min-pruning="$advanced.min_pruning"
+            --minimum-allele-fraction="$advanced.minimum_allele_fraction"
             --num-pruning-samples="$advanced.num_pruning_samples"
             --pair-hmm-gap-continuation-penalty="$advanced.pair_hmm_gap_continuation_penalty"
             --pair-hmm-implementation="$advanced.pair_hmm_implementation"
             --pcr-indel-model="$advanced.pcr_indel_model"
             --phred-scaled-global-read-mismapping-rate="$advanced.phred_scaled_global_read_mismapping_rate"
+            --pruning-lod-threshold="$advanced.pruning_lod_threshold"
             --smith-waterman="$advanced.smith_waterman"
-            $advanced.all_site_pls
             $advanced.allow_non_unique_kmers_in_ref
-            $advanced.consensus
+            $advanced.disable_adaptive_pruning
             $advanced.disable_tool_default_annotations
-            $advanced.do_not_run_physical_phasing
+            $advanced.disable_tool_default_read_filters
             $advanced.dont_increase_kmer_sizes_for_cycles
             $advanced.dont_trim_active_regions
             $advanced.dont_use_soft_clipped_bases
             $advanced.enable_all_annotations
-            $advanced.genotype_filtered_alleles
+            $advanced.force_active
+            $advanced.force_call_filtered_alleles
+            $advanced.independent_mates
+            $advanced.recover_all_dangling_branches
             $advanced.use_filtered_reads_for_annotations
 
         #end if
@@ -265,85 +284,17 @@
         <expand macro="gatk_bam_req_params"/>
         <expand macro="gzip_vcf_params"/>
         <expand macro="ref_sel"/>
-        <conditional name="common">
-            <param name="common_parameters" type="select" label="Common parameters">
-                <option value="no">Use internal defaults</option>
-                <option value="yes">Specify parameters</option>
-            </param>
-            <when value="yes">
-                <expand macro="gatk_excl_ints"/>
-                <expand macro="seq_dict_sel"/>
-                <param name="add_output_sam_program_record" argument="--add-output-sam-program-record" type="boolean" truevalue="--add-output-sam-program-record" falsevalue="" optional="true" checked="true" label="Add Output Sam Program Record" help="If true, adds a PG tag to created SAM/BAM/CRAM files."/>
-                <param name="add_output_vcf_command_line" argument="--add-output-vcf-command-line" type="boolean" truevalue="--add-output-vcf-command-line" falsevalue="" optional="true" checked="true" label="Add Output Vcf Command Line" help="If true, adds a command line header line to created VCF files."/>
-                <param name="disable_read_filter" argument="--disable-read-filter" type="select" multiple="true" value="" label="Disable Read Filter" help="Read filters to be disabled before analysis">
-                    <option value="GoodCigarReadFilter">Good cigar string</option>
-                    <option value="MappedReadFilter">Mapped read</option>
-                    <option value="MappingQualityAvailableReadFilter">Mapping quality available</option>
-                    <option value="MappingQualityNotZeroReadFilter">Mapping quality not zero</option>
-                    <option value="NonChimericOriginalAlignmentReadFilter">Non-chimeric original alignment</option>
-                    <option value="NonZeroReferenceLengthAlignmentReadFilter">Non-zero reference length alignment</option>
-                    <option value="NotDuplicateReadFilter">Not a duplicate read</option>
-                    <option value="NotSecondaryAlignmentReadFilter">Not a secondary alignment</option>
-                    <option value="PassesVendorQualityCheckReadFilter">Passes vendor quality check</option>
-                    <option value="WellformedReadFilter">Well-formed read</option>
-                </param>
-                <param name="disable_tool_default_read_filters" argument="--disable-tool-default-read-filters" type="boolean" truevalue="--disable-tool-default-read-filters" falsevalue="" optional="true" checked="false" label="Disable Tool Default Read Filters" help="Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)"/>
-                <param name="interval_set_rule" argument="--interval-set-rule" type="select" optional="true" label="Interval Set Rule" help="Set merging approach to use for combining interval inputs">
-                    <option selected="true" value="UNION">Union</option>
-                    <option value="INTERSECTION">Intersection</option>
-                </param>
-                <param name="lenient" argument="--lenient" type="boolean" truevalue="--lenient" falsevalue="" optional="true" checked="false" label="Lenient" help="Lenient processing of VCF files"/>
-                <param name="read_filter" argument="--read-filter" type="select" multiple="true" value="" label="Read Filter" help="Read filters to be applied before analysis">
-                    <option value="AlignmentAgreesWithHeaderReadFilter">Alignment agrees with header</option>
-                    <option value="AllowAllReadsReadFilter">Allow all reads</option>
-                    <option value="AmbiguousBaseReadFilter">Ambiguous base</option>
-                    <option value="CigarContainsNoNOperator">Cigar contains no NO operator</option>
-                    <option value="FirstOfPairReadFilter">First of pair</option>
-                    <option value="GoodCigarReadFilter">Good cigar string</option>
-                    <option value="HasReadGroupReadFilter">Has read group</option>
-                    <option value="MappedReadFilter">Mapped read</option>
-                    <option value="MappingQualityAvailableReadFilter">Mapping quality available</option>
-                    <option value="MappingQualityNotZeroReadFilter">Mapping quality not zero</option>
-                    <option value="MatchingBasesAndQualsReadFilter">Matching bases and quals</option>
-                    <option value="MateDifferentStrandReadFilter">Mate different strand</option>
-                    <option value="MateOnSameContigOrNoMappedMateReadFilter">Mate on same contig or no mapped mate</option>
-                    <option value="MateUnmappedAndUnmappedReadFilter">Mate unmapped and mapped</option>
-                    <option value="MetricsReadFilter">Metrics</option>
-                    <option value="NonChimericOriginalAlignmentReadFilter">Non-chimeric original alignment</option>
-                    <option value="NonZeroFragmentLengthReadFilter">Non-zero fragment length</option>
-                    <option value="NonZeroReferenceLengthAlignmentReadFilter">Non-zero reference length alignment</option>
-                    <option value="NotDuplicateReadFilter">Not duplicate</option>
-                    <option value="NotOpticalDuplicateReadFilter">Not optical duplicate</option>
-                    <option value="NotSecondaryAlignmentReadFilter">Not a secondary alignment</option>
-                    <option value="NotSupplementaryAlignmentReadFilter">Not a supplementary alignment</option>
-                    <option value="OverclippedReadFilter">Overclipped</option>
-                    <option value="PairedReadFilter">Paired</option>
-                    <option value="PassesVendorQualityCheckReadFilter">Passes vendor quality check</option>
-                    <option value="PrimaryLineReadFilter">Primary line</option>
-                    <option value="ProperlyPairedReadFilter">Properly paired</option>
-                    <option value="ReadLengthEqualsCigarLengthReadFilter">Read length equals cigar length</option>
-                    <option value="SecondOfPairReadFilter">Second of pair</option>
-                    <option value="SeqIsStoredReadFilter">Sequence is stored</option>
-                    <option value="SoftClippedReadFilter">Soft clipped</option>
-                    <option value="ValidAlignmentStartReadFilter">Valid alignment start</option>
-                    <option value="ValidAlignmentEndReadFilter">Valid alignment end</option>
-                    <option value="WellformedReadFilter">Well-formed read</option>
-                </param>
-                <param name="read_validation_stringency" argument="--read-validation-stringency" type="select" optional="true" label="Read Validation Stringency" help="Validation stringency for all SAM/BAM/CRAM/SRA files read by this program.  The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.">
-                    <option selected="true" value="SILENT">Silent</option>
-                    <option value="STRICT">Strict</option>
-                    <option value="LENIENT">Lenient</option>
-                </param>
-            </when>
-            <when value="no" />
-        </conditional>
         <conditional name="optional">
             <param name="optional_parameters" type="select" label="Optional parameters">
                 <option value="no">Use internal defaults</option>
                 <option value="yes">Specify parameters</option>
             </param>
             <when value="yes">
+                <expand macro="gatk_excl_ints"/>
                 <expand macro="gatk_ints"/>
+                <expand macro="seq_dict_sel"/>
+                <param name="add_output_sam_program_record" argument="--add-output-sam-program-record" type="boolean" truevalue="--add-output-sam-program-record" falsevalue="" optional="true" checked="true" label="Add Output Sam Program Record" help="If true, adds a PG tag to created SAM/BAM/CRAM files."/>
+                <param name="add_output_vcf_command_line" argument="--add-output-vcf-command-line" type="boolean" truevalue="--add-output-vcf-command-line" falsevalue="" optional="true" checked="true" label="Add Output Vcf Command Line" help="If true, adds a command line header line to created VCF files."/>
                 <param name="af_of_alleles_not_in_resource" argument="--af-of-alleles-not-in-resource" type="float" optional="true" value="-1.0" label="Af Of Alleles Not In Resource" help="Population allele fraction assigned to alleles not found in germline resource.  Please see docs/mutect/mutect2.pdf fora derivation of the default value."/>
                 <param name="annotate_with_num_discovered_alleles" argument="--annotate-with-num-discovered-alleles" type="boolean" truevalue="--annotate-with-num-discovered-alleles" falsevalue="" optional="true" checked="false" label="Annotate With Num Discovered Alleles" help="If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site"/>
                 <param argument="--annotation" type="select" multiple="true" label="Annotations" help="One or more specific annotations to add to variant calls">
@@ -440,10 +391,62 @@
                 </param>
                 <param name="pedigree" argument="--pedigree" type="data" optional="true" format="vcf,vcf_bgzip" label="Pedigree" help="Pedigree file for determining the population &quot;founders&quot;. If a file is provided here, a pedigree-based annotation must be added above."/>
                 <param name="base_quality_score_threshold" argument="--base-quality-score-threshold" type="integer" optional="true" value="18" label="Base Quality Score Threshold" help="Base qualities below this threshold will be reduced to the minimum (6)"/>
+                <param name="callable_depth" argument="--callable-depth" type="integer" optional="true" value="10" label="Minimum depth to be considered callable" help="Does not affect genotyping"/>
                 <param name="contamination_fraction_to_filter" argument="--contamination-fraction-to-filter" type="float" optional="true" value="0.0" label="Contamination Fraction To Filter" help="Fraction of contamination in sequencing data (for all samples) to aggressively remove"/>
                 <param name="disable_bam_index_caching" argument="--disable-bam-index-caching" type="boolean" truevalue="--disable-bam-index-caching" falsevalue="" optional="true" checked="false" label="Disable Bam Index Caching" help="If true, don&amp;apos;t cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified.  Caching is automatically disabled if there are no intervals specified."/>
+                <param name="disable_read_filter" argument="--disable-read-filter" type="select" multiple="true" value="" label="Disable Read Filter" help="Read filters to be disabled before analysis">
+                    <option value="GoodCigarReadFilter">Good cigar string</option>
+                    <option value="MappedReadFilter">Mapped read</option>
+                    <option value="MappingQualityAvailableReadFilter">Mapping quality available</option>
+                    <option value="MappingQualityNotZeroReadFilter">Mapping quality not zero</option>
+                    <option value="NonChimericOriginalAlignmentReadFilter">Non-chimeric original alignment</option>
+                    <option value="NonZeroReferenceLengthAlignmentReadFilter">Non-zero reference length alignment</option>
+                    <option value="NotDuplicateReadFilter">Not a duplicate read</option>
+                    <option value="NotSecondaryAlignmentReadFilter">Not a secondary alignment</option>
+                    <option value="PassesVendorQualityCheckReadFilter">Passes vendor quality check</option>
+                    <option value="WellformedReadFilter">Well-formed read</option>
+                </param>
+                <param name="read_filter" argument="--read-filter" type="select" multiple="true" value="" label="Read Filter" help="Read filters to be applied before analysis">
+                    <option value="AlignmentAgreesWithHeaderReadFilter">Alignment agrees with header</option>
+                    <option value="AllowAllReadsReadFilter">Allow all reads</option>
+                    <option value="AmbiguousBaseReadFilter">Ambiguous base</option>
+                    <option value="CigarContainsNoNOperator">Cigar contains no NO operator</option>
+                    <option value="FirstOfPairReadFilter">First of pair</option>
+                    <option value="GoodCigarReadFilter">Good cigar string</option>
+                    <option value="HasReadGroupReadFilter">Has read group</option>
+                    <option value="MappedReadFilter">Mapped read</option>
+                    <option value="MappingQualityAvailableReadFilter">Mapping quality available</option>
+                    <option value="MappingQualityNotZeroReadFilter">Mapping quality not zero</option>
+                    <option value="MatchingBasesAndQualsReadFilter">Matching bases and quals</option>
+                    <option value="MateDifferentStrandReadFilter">Mate different strand</option>
+                    <option value="MateOnSameContigOrNoMappedMateReadFilter">Mate on same contig or no mapped mate</option>
+                    <option value="MateUnmappedAndUnmappedReadFilter">Mate unmapped and mapped</option>
+                    <option value="MetricsReadFilter">Metrics</option>
+                    <option value="NonChimericOriginalAlignmentReadFilter">Non-chimeric original alignment</option>
+                    <option value="NonZeroFragmentLengthReadFilter">Non-zero fragment length</option>
+                    <option value="NonZeroReferenceLengthAlignmentReadFilter">Non-zero reference length alignment</option>
+                    <option value="NotDuplicateReadFilter">Not duplicate</option>
+                    <option value="NotOpticalDuplicateReadFilter">Not optical duplicate</option>
+                    <option value="NotSecondaryAlignmentReadFilter">Not a secondary alignment</option>
+                    <option value="NotSupplementaryAlignmentReadFilter">Not a supplementary alignment</option>
+                    <option value="OverclippedReadFilter">Overclipped</option>
+                    <option value="PairedReadFilter">Paired</option>
+                    <option value="PassesVendorQualityCheckReadFilter">Passes vendor quality check</option>
+                    <option value="PrimaryLineReadFilter">Primary line</option>
+                    <option value="ProperlyPairedReadFilter">Properly paired</option>
+                    <option value="ReadLengthEqualsCigarLengthReadFilter">Read length equals cigar length</option>
+                    <option value="SecondOfPairReadFilter">Second of pair</option>
+                    <option value="SeqIsStoredReadFilter">Sequence is stored</option>
+                    <option value="SoftClippedReadFilter">Soft clipped</option>
+                    <option value="ValidAlignmentStartReadFilter">Valid alignment start</option>
+                    <option value="ValidAlignmentEndReadFilter">Valid alignment end</option>
+                    <option value="WellformedReadFilter">Well-formed read</option>
+                </param>
                 <param name="disable_sequence_dictionary_validation" argument="--disable-sequence-dictionary-validation" type="boolean" truevalue="--disable-sequence-dictionary-validation" falsevalue="" optional="true" checked="false" label="Disable Sequence Dictionary Validation" help="If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!"/>
                 <param name="downsampling_stride" argument="--downsampling-stride" type="integer" optional="true" value="1" label="Downsampling Stride" help="Downsample a pool of reads starting within a range of one or more bases."/>
+                <param name="f1r2_max_depth" argument="--f1r2-max-depth" type="integer" optional="true" value="200" label="Sites with depth higher than this value will be grouped" />
+                <param name="f1r2_median_mq" argument="--f1r2-median-mq" type="integer" optional="true" value="50" label="Skip sites with median mapping quality below this value" />
+                <param name="f1r2_min_bq" argument="--base-quality-score-threshold" type="integer" optional="true" value="20" label="Exclude bases below this quality from pileup" />
                 <param name="founder_id" argument="--founder-id" type="text" optional="true" value="" label="Founder Id" help="Samples representing the population &amp;quot;founders&amp;quot;"/>
                 <param name="gcs_max_retries" argument="--gcs-max-retries" type="integer" optional="true" value="20" label="Gcs Max Retries" help="If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection"/>
                 <param name="genotype_germline_sites" argument="--genotype-germline-sites" type="boolean" truevalue="--genotype-germline-sites" falsevalue="" optional="true" checked="false" label="Genotype Germline Sites" help="(EXPERIMENTAL) Call all apparent germline site even though they will ultimately be filtered."/>
@@ -452,32 +455,38 @@
                 <param name="germline_resource" argument="--germline-resource" type="data" optional="true" format="vcf,vcf_bgzip" label="Germline Resource" help="Population vcf of germline sequencing containing allele fractions."/>
                 <param name="heterozygosity" argument="--heterozygosity" type="float" optional="true" value="0.001" label="Heterozygosity" help="The expected heterozygosity value used to compute prior probability that a locus is non-reference. The default priors are for provided for humans: het = 1e-3 which means that the probability of N samples being hom-ref at a site is: 1 - sum_i_2N (het / i) Note that heterozygosity as used here is the population genetics concept: http://en.wikipedia.org/wiki/Zygosity#Heterozygosity_in_population_genetics That is, a hets value of 0.01 implies that two randomly chosen chromosomes from the population of organisms would differ from each other (one being A and the other B) at a rate of 1 in 100 bp. Note that this quantity has nothing to do with the likelihood of any given sample having a heterozygous genotype, which in the GATK is purely determined by the probability of the observed data P(D | AB) under the model that there may be a AB het genotype. The posterior probability of this AB genotype would use the het prior, but the GATK only uses this posterior probability in determining the prob. that a site is polymorphic. So changing the het parameters only increases the chance that a site will be called non-reference across all samples, but doesn't actually change the output genotype likelihoods at all, as these aren't posterior probabilities at all. The quantity that changes whether the GATK considers the possibility of a het genotype at all is the ploidy, which determines how many chromosomes each individual in the species carries."/>
                 <param name="heterozygosity_stdev" argument="--heterozygosity-stdev" type="float" optional="true" value="0.01" label="Heterozygosity Stdev" help="Standard deviation of heterozygosity for SNP and indel calling."/>
+                <param name="ignore_itr_artifacts" argument="--ignore-itr-artifacts" type="boolean" truevalue="--ignore-itr-artifacts" falsevalue="" optional="true" checked="false" label="Turn off read transformer that clips artifacts associated with end repair insertions near inverted tandem repeats" />
                 <param name="indel_heterozygosity" argument="--indel-heterozygosity" type="float" optional="true" value="0.000125" label="Indel Heterozygosity" help="Heterozygosity for indel calling.  See the GATKDocs for heterozygosity for full details on the meaning of this population genetics concept"/>
                 <param name="initial_tumor_lod" argument="--initial-tumor-lod" type="float" optional="true" value="2.0" label="Initial Tumor Lod" help="LOD threshold to consider pileup active."/>
+                <param name="interval_exclusion_padding" argument="--interval-exclusion-padding" type="integer" value="0" label="Interval exclusion padding" help="Amount of padding (in bp) to add to each interval you are excluding" />
+                <param name="interval_padding" argument="--interval-padding" type="integer" value="0" label="Interval padding" help="Amount of padding (in bp) to add to each interval you are including" />
                 <param name="interval_merging_rule" argument="--interval-merging-rule" type="select" optional="true" label="Interval Merging Rule" help="Interval merging rule for abutting intervals">
                     <option selected="true" value="ALL">All</option>
                     <option value="OVERLAPPING_ONLY">Overlapping only</option>
                 </param>
+                <param name="interval_set_rule" argument="--interval-set-rule" type="select" optional="true" label="Interval Set Rule" help="Set merging approach to use for combining interval inputs">
+                    <option selected="true" value="UNION">Union</option>
+                    <option value="INTERSECTION">Intersection</option>
+                </param>
+                <param name="lenient" argument="--lenient" type="boolean" truevalue="--lenient" falsevalue="" optional="true" checked="false" label="Lenient" help="Lenient processing of VCF files"/>
                 <param name="max_population_af" argument="--max-population-af" type="float" optional="true" value="0.01" label="Max Population Af" help="Maximum population allele frequency in tumor-only mode."/>
                 <param name="max_reads_per_alignment_start" argument="--max-reads-per-alignment-start" type="integer" optional="true" value="50" label="Max Reads Per Alignment Start" help="Maximum number of reads to retain per alignment start position. Reads above this threshold will be downsampled. Set to 0 to disable."/>
                 <param name="min_base_quality_score" argument="--min-base-quality-score" type="integer" optional="true" value="10" label="Min Base Quality Score" help="Minimum base quality required to consider a base for calling"/>
+                <param name="mitochondria_mode" argument="--mitochondria-mode" type="boolean" truevalue="--mitochondria-mode" falsevalue="" label="Mitochondria mode sets emission and initial LODs to 0" />
                 <param name="native_pair_hmm_use_double_precision" argument="--native-pair-hmm-use-double-precision" type="boolean" truevalue="--native-pair-hmm-use-double-precision" falsevalue="" optional="true" checked="false" label="Native Pair Hmm Use Double Precision" help="use double precision in the native pairHmm. This is slower but matches the java implementation better"/>
                 <param name="normal_lod" argument="--normal-lod" type="float" optional="true" value="2.2" label="Normal Lod" help="LOD threshold for calling normal variant non-germline."/>
                 <param name="normal_sample" argument="--normal-sample" type="text" optional="true" value="" label="Normal Sample" help="BAM sample name of normal.  May be URL-encoded as output by GetSampleName with -encode argument."/>
-                <param name="num_reference_samples_if_no_call" argument="--num-reference-samples-if-no-call" type="integer" optional="true" value="0" label="Num Reference Samples If No Call" help="Number of hom-ref genotypes to infer at sites not present in a panel"/>
-                <param name="output_mode" argument="--output-mode" type="select" optional="true" label="Output Mode" help="Specifies which type of calls we should output">
-                    <option selected="true" value="EMIT_VARIANTS_ONLY">Variants only</option>
-                    <option value="EMIT_ALL_CONFIDENT_SITES">All confident sites</option>
-                    <option value="EMIT_ALL_SITES">All sites</option>
+                <param name="panel_of_normals" argument="--panel-of-normals" type="data" optional="true" format="vcf,vcf_bgzip" label="Panel Of Normals" help="VCF file of sites observed in normal."/>
+                <param name="pcr_indel_qual" argument="--pcr-indel-qual" type="integer" optional="true" value="40" label="Phred-scaled PCR indel qual for overlapping fragments" />
+                <param name="pcr_snv_qual" argument="--pcr-snv-qual" type="integer" optional="true" value="40" label="Phred-scaled PCR SNV qual for overlapping fragments" />
+                <param name="sites_only_vcf_output" argument="--sites-only-vcf-output" type="boolean" truevalue="--sites-only-vcf-output" falsevalue="" optional="true" checked="false" label="Sites Only Vcf Output" help="If true, don&apos;t emit genotype fields when writing vcf file output."/>
+                <param name="read_validation_stringency" argument="--read-validation-stringency" type="select" optional="true" label="Read Validation Stringency" help="Validation stringency for all SAM/BAM/CRAM/SRA files read by this program.  The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.">
+                    <option selected="true" value="SILENT">Silent</option>
+                    <option value="STRICT">Strict</option>
+                    <option value="LENIENT">Lenient</option>
                 </param>
-                <param name="panel_of_normals" argument="--panel-of-normals" type="data" optional="true" format="vcf,vcf_bgzip" label="Panel Of Normals" help="VCF file of sites observed in normal."/>
-                <param name="sites_only_vcf_output" argument="--sites-only-vcf-output" type="boolean" truevalue="--sites-only-vcf-output" falsevalue="" optional="true" checked="false" label="Sites Only Vcf Output" help="If true, don&apos;t emit genotype fields when writing vcf file output."/>
-                <param name="population_callset" argument="--population-callset" type="data" optional="true" format="" label="Population Callset" help="Callset to use in calculating genotype priors"/>
-                <param name="sample_ploidy" argument="--sample-ploidy" type="integer" optional="true" value="2" label="Sample Ploidy" help="Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy)."/>
                 <param name="sites_only_vcf_output" argument="--sites-only-vcf-output" type="boolean" truevalue="--sites-only-vcf-output" falsevalue="" optional="true" checked="false" label="Sites Only Vcf Output" help="If true, don&amp;apos;t emit genotype fields when writing vcf file output."/>
-                <param name="standard_min_confidence_threshold_for_calling" argument="--standard-min-confidence-threshold-for-calling" type="float" optional="true" value="10.0" label="Standard Min Confidence Threshold For Calling" help="The minimum phred-scaled confidence threshold at which variants should be called"/>
                 <param name="tumor_lod_to_emit" argument="--tumor-lod-to-emit" type="float" optional="true" value="3.0" label="Tumor Lod To Emit" help="LOD threshold to emit tumor variant to VCF."/>
-                <param name="use_new_qual_calculator" argument="--use-new-qual-calculator" type="boolean" truevalue="--use-new-qual-calculator" falsevalue="" optional="true" checked="false" label="Use New Qual Calculator" help="If provided, we will use the new AF model instead of the so-called exact model"/>
             </when>
             <when value="no" />
         </conditional>
@@ -488,31 +497,40 @@
             </param>
             <when value="yes">
                 <param name="active_probability_threshold" argument="--active-probability-threshold" type="float" optional="true" value="0.002" label="Active Probability Threshold" help="Minimum probability for a locus to be considered active."/>
-                <param name="all_site_pls" argument="--all-site-pls" type="boolean" truevalue="--all-site-pls" falsevalue="" optional="true" checked="false" label="All Site Pls" help="Annotate all sites with PLs"/>
                 <param name="allow_non_unique_kmers_in_ref" argument="--allow-non-unique-kmers-in-ref" type="boolean" truevalue="--allow-non-unique-kmers-in-ref" falsevalue="" optional="true" checked="false" label="Allow Non Unique Kmers In Ref" help="Allow graphs that have non-unique kmers in the reference"/>
                 <param name="assembly_region_padding" argument="--assembly-region-padding" type="integer" optional="true" value="100" label="Assembly Region Padding" help="Number of additional bases of context to include around each assembly region"/>
                 <param name="bam_writer_type" argument="--bam-writer-type" type="select" optional="true" label="Bam Writer Type" help="Which haplotypes should be written to the BAM">
                     <option selected="true" value="CALLED_HAPLOTYPES">Called haplotypes</option>
                     <option value="ALL_POSSIBLE_HAPLOTYPES">All possible haplotypes</option>
                 </param>
-                <param name="consensus" argument="--consensus" type="boolean" truevalue="--consensus" falsevalue="" optional="true" checked="false" label="Consensus" help="1000G consensus mode"/>
-                <param name="disable_tool_default_annotations" argument="--disable-tool-default-annotations" type="boolean" truevalue="--disable-tool-default-annotations" falsevalue="" optional="true" checked="false" label="Disable Tool Default Annotations" help="Disable all tool default annotations"/>
-                <param name="do_not_run_physical_phasing" argument="--do-not-run-physical-phasing" type="boolean" truevalue="--do-not-run-physical-phasing" falsevalue="" optional="true" checked="false" label="Do Not Run Physical Phasing" help="Disable physical phasing"/>
+
+                <param name="disable_adaptive_pruning" argument="--disable-adaptive-pruning" type="boolean" truevalue="--disable-adaptive-pruning" falsevalue="" optional="true" checked="false" label="Disable adaptive pruning" help="Disable the adaptive algorithm for pruning paths in the graph"/>
+                <param name="disable_tool_default_annotations" argument="--disable-tool-default-annotations" type="boolean" truevalue="--disable-tool-default-annotations" falsevalue="" optional="true" checked="false" label="Disable Default Annotations" help="Disable all tool default annotations"/>
+                <param name="disable_tool_default_read_filters" argument="--disable-tool-default-read-filters" type="boolean" truevalue="--disable-tool-default-read-filters" falsevalue="" optional="true" checked="false" label="Disable default read filters" help="WARNING: many tools will not function correctly without their default read filters on"/>
                 <param name="dont_increase_kmer_sizes_for_cycles" argument="--dont-increase-kmer-sizes-for-cycles" type="boolean" truevalue="--dont-increase-kmer-sizes-for-cycles" falsevalue="" optional="true" checked="false" label="Dont Increase Kmer Sizes For Cycles" help="Disable iterating over kmer sizes when graph cycles are detected"/>
                 <param name="dont_trim_active_regions" argument="--dont-trim-active-regions" type="boolean" truevalue="--dont-trim-active-regions" falsevalue="" optional="true" checked="false" label="Dont Trim Active Regions" help="If specified, we will not trim down the active region from the full region (active + extension) to just the active interval for genotyping"/>
                 <param name="dont_use_soft_clipped_bases" argument="--dont-use-soft-clipped-bases" type="boolean" truevalue="--dont-use-soft-clipped-bases" falsevalue="" optional="true" checked="false" label="Dont Use Soft Clipped Bases" help="Do not analyze soft clipped bases in the reads"/>
+                <param name="emit_ref_confidence" argument="--emit-ref-confidence" type="select" label="Mode for emitting reference confidence scores" help="NOTE: This is a beta feature in Mutect2">
+                    <option value="NONE">None</option>
+                    <option value="BP_RESOLUTION">Basepair resolution</option>
+                    <option value="GVCF">Genomic VCF</option>
+                </param>
                 <param name="enable_all_annotations" argument="--enable-all-annotations" type="boolean" truevalue="--enable-all-annotations" falsevalue="" optional="true" checked="false" label="Enable All Annotations" help="Use all possible annotations (not for the faint of heart)"/>
-                <param name="genotype_filtered_alleles" argument="--genotype-filtered-alleles" type="boolean" truevalue="--genotype-filtered-alleles" falsevalue="" optional="true" checked="false" label="Genotype Filtered Alleles" help="Whether to genotype all given alleles, even filtered ones, --genotyping_mode is GENOTYPE_GIVEN_ALLELES"/>
-                <param name="input_prior" argument="--input-prior" type="float" optional="true" value="" label="Input Prior" help="By default, the prior specified with the heterozygosity argument is used for variant discovery at a particular locus, using an infinite sites model, see e.g. Waterson (1975) or Tajima (1996). This model asserts that the probability of having a population of k variant sites in N chromosomes is proportional to theta/k, for 1=1:N There are instances where using this prior might not be desireable, e.g. for population studies where prior might not be appropriate, as for example when the ancestral status of the reference allele is not known. By using this argument, user can manually specify priors to be used for calling as a vector for doubles, with the following restriciotns: a) User must specify 2N values, where N is the number of samples. b) Only diploid calls supported. c) Probability values are specified in double format, in linear space. d) No negative values allowed. e) Values will be added and Pr(AC=0) will be 1-sum, so that they sum up to one. f) If user-defined values add to more than one, an error will be produced. If user wants completely flat priors, then user should specify the same value (=1/(2*N+1)) 2*N times,e.g. -inputPrior 0.33 -inputPrior 0.33 for the single-sample diploid case."/>
+                <param name="force_active" argument="--force-active" type="boolean" truevalue="--force-active" falsevalue="" optional="true" checked="false" label="Mark all regions active" help="If selected, all regions will be marked as active"/>
+                <param name="force_call_filtered_alleles" argument="--force-call-filtered-alleles" type="boolean" truevalue="--force-call-filtered-alleles" falsevalue="" optional="true" checked="false" label="Force-call filtered alleles" help="Force-call filtered alleles included in the resource specified by --alleles"/>
+                <param name="gvcf_lod_band" argument="--gvcf-lod-band" type="float" optional="true" label="Upper bounds for reference confidence" help="Exclusive upper bounds for reference confidence LOD bands (must be specified in increasing order)" />
+                <param name="independent_mates" argument="--independent-mates" type="boolean" truevalue="--independent-mates" falsevalue="" label="Independent mates" help="Allow paired reads to independently support different haplotypes. Useful for validations with ill-designed synthetic data" />
                 <param name="kmer_size" argument="--kmer-size" type="integer" optional="true" value="" label="Kmer Size" help="Kmer size to use in the read threading assembler"/>
                 <param name="max_assembly_region_size" argument="--max-assembly-region-size" type="integer" optional="true" value="300" label="Max Assembly Region Size" help="Maximum size of an assembly region"/>
                 <param name="max_mnp_distance" argument="--max-mnp-distance" type="integer" optional="true" value="1" label="Max Mnp Distance" help="Two or more phased substitutions separated by this distance or less are merged into MNPs."/>
                 <param name="max_num_haplotypes_in_population" argument="--max-num-haplotypes-in-population" type="integer" optional="true" value="128" label="Max Num Haplotypes In Population" help="Maximum number of haplotypes to consider for your population"/>
                 <param name="max_prob_propagation_distance" argument="--max-prob-propagation-distance" type="integer" optional="true" value="50" label="Max Prob Propagation Distance" help="Upper limit on how many bases away probability mass can be moved around when calculating the boundaries between active and inactive assembly regions"/>
                 <param name="max_suspicious_reads_per_alignment_start" argument="--max-suspicious-reads-per-alignment-start" type="integer" optional="true" value="0" label="Max Suspicious Reads Per Alignment Start" help="Maximum number of suspicious reads (mediocre mapping quality or too many substitutions) allowed in a downsampling stride.  Set to 0 to disable."/>
+                <param name="max_unpruned_variants" argument="--max-unpruned-variants" type="integer" optional="true" value="100" label="Maximum number of variants" help="Maximum number of variants in graph the adaptive pruner will allow"/>
                 <param name="min_assembly_region_size" argument="--min-assembly-region-size" type="integer" optional="true" value="50" label="Min Assembly Region Size" help="Minimum size of an assembly region"/>
                 <param name="min_dangling_branch_length" argument="--min-dangling-branch-length" type="integer" optional="true" value="4" label="Min Dangling Branch Length" help="Minimum length of a dangling branch to attempt recovery"/>
                 <param name="min_pruning" argument="--min-pruning" type="integer" optional="true" value="2" label="Min Pruning" help="Minimum support to not prune paths in the graph"/>
+                <param name="minimum_allele_fraction" argument="--minimum-allele-fraction" type="float" optional="true" value="0.0" label="Fractions to consider" help="Lower bound of variant allele fractions to consider when calculating variant LOD"/>
                 <param name="num_pruning_samples" argument="--num-pruning-samples" type="integer" optional="true" value="1" label="Num Pruning Samples" help="Number of samples that must pass the minPruning threshold"/>
                 <param name="pair_hmm_gap_continuation_penalty" argument="--pair-hmm-gap-continuation-penalty" type="integer" optional="true" value="10" label="Pair Hmm Gap Continuation Penalty" help="Flat gap continuation penalty for use in the Pair HMM"/>
                 <param name="pair_hmm_implementation" argument="--pair-hmm-implementation" type="select" optional="true" label="Pair Hmm Implementation" help="The PairHMM implementation to use for genotype likelihood calculations">
@@ -531,6 +549,8 @@
                     <option value="AGGRESSIVE">Aggressive</option>
                 </param>
                 <param name="phred_scaled_global_read_mismapping_rate" argument="--phred-scaled-global-read-mismapping-rate" type="integer" optional="true" value="45" label="Phred Scaled Global Read Mismapping Rate" help="The global assumed mismapping rate for reads"/>
+                <param name="pruning_lod_threshold" argument="--pruning-lod-threshold" type="float" optional="true" value="2.302585092994046" label="Pruning LOD threshold" help="Likelihood ratio threshold for adaptive pruning algorithm" />
+                <param name="recover_all_dangling_branches" argument="--recover-all-dangling-branches" type="boolean" truevalue="--recover-all-dangling-branches" falsevalue="" label="Recover all dangling branches" />
                 <param name="smith_waterman" argument="--smith-waterman" type="select" optional="true" label="Smith Waterman" help="Which Smith-Waterman implementation to use, generally 'Fastest available' is the right choice">
                     <option selected="true" value="FASTEST_AVAILABLE">Fastest available</option>
                     <option value="AVX_ENABLED">AVX-Enabled</option>
@@ -571,7 +591,6 @@
             <param name="reference_sequence" ftype="fasta" value="reference.fa" />
             <param name="gzipped_output" value="false" />
             <param name="reference_source_selector" value="history" />
-            <param name="common_parameters" value="no" />
             <param name="optional_parameters" value="no" />
             <param name="advanced_parameters" value="no" />
             <param name="output_parameters" value="no" />
@@ -582,7 +601,6 @@
             <param name="reference_sequence" ftype="fasta" value="reference.fa" />
             <param name="gzipped_output" value="false" />
             <param name="reference_source_selector" value="history" />
-            <param name="common_parameters" value="yes" />
             <param name="read_filter" value="AmbiguousBaseReadFilter,FirstOfPairReadFilter,GoodCigarReadFilter" />
             <param name="seqdict_source" value="history" />
             <param name="seqdict_sequence" value="Mutect2-in2.dict" />
@@ -596,7 +614,6 @@
             <param name="reference_sequence" ftype="fasta" value="reference.fa" />
             <param name="gzipped_output" value="false" />
             <param name="reference_source_selector" value="history" />
-            <param name="common_parameters" value="no" />
             <param name="optional_parameters" value="yes" />
             <param name="annotation" value="StrandBiasBySample,BaseQualityHistogram,OrientationBiasReadCounts" />
             <param name="annotation_group" value="StandardMutectAnnotation" />
@@ -609,7 +626,6 @@
             <param name="reference_sequence" ftype="fasta" value="reference.fa" />
             <param name="gzipped_output" value="false" />
             <param name="reference_source_selector" value="history" />
-            <param name="common_parameters" value="no" />
             <param name="optional_parameters" value="yes" />
             <param name="advanced_parameters" value="yes" />
             <param name="dont_trim_active_regions" value="true" />
@@ -621,7 +637,6 @@
             <param name="reference_sequence" ftype="fasta" value="reference.fa" />
             <param name="gzipped_output" value="false" />
             <param name="reference_source_selector" value="history" />
-            <param name="common_parameters" value="no" />
             <param name="optional_parameters" value="no" />
             <param name="advanced_parameters" value="no" />
             <param name="output_parameters" value="yes" />
diff -r f41a1e03538b -r fd2d6e035c3f macros.xml
--- a/macros.xml	Wed Oct 30 15:33:59 2019 -0400
+++ b/macros.xml	Mon Nov 18 13:45:47 2019 -0500
@@ -22,7 +22,7 @@
 
     <!--Define sections that parameters could exist within.-->
     <template name="set_sections">
-        #set global $sections = ['', 'optional.', 'advanced.', 'common.', 'deprecated.']
+        #set global $sections = ['', 'optional.', 'advanced.', 'deprecated.']
     </template>
 
     <!--Reference genome handling-->
@@ -671,7 +671,7 @@
 
 
     <!--<template name="ref_opts">-->
-        <!--#set $sections = ['optional','advanced','common','deprecated','']-->
+        <!--#set $sections = ['optional','advanced','deprecated','']-->
         <!--#silent $sys.stderr.write("I WOULD LIKE TO SHOW THE SECTION VARIABLE: '${sections}'\n")-->
         <!--#for $sect in $sections-->
             <!--#if $varExists('$sect.reference_source.reference_source_selector')-->
diff -r f41a1e03538b -r fd2d6e035c3f test-data/Mutect2-out1.vcf
--- a/test-data/Mutect2-out1.vcf	Wed Oct 30 15:33:59 2019 -0400
+++ b/test-data/Mutect2-out1.vcf	Mon Nov 18 13:45:47 2019 -0500
@@ -11,7 +11,7 @@
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
 ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2  --tumor-sample SRR8525881 --output output.vcf --input input.bam --reference reference.fa --QUIET true  --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --dont-trim-active-regions false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.4.0",Date="October 29, 2019 1:13:39 PM EDT">
+##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2  --tumor-sample SRR8525881 --output output.vcf --input input.bam --reference reference.fa --QUIET true  --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --dont-trim-active-regions false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.4.0",Date="November 15, 2019 4:24:40 PM EST">
 ##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination">
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
 ##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype">
diff -r f41a1e03538b -r fd2d6e035c3f test-data/Mutect2-out2.vcf
--- a/test-data/Mutect2-out2.vcf	Wed Oct 30 15:33:59 2019 -0400
+++ b/test-data/Mutect2-out2.vcf	Mon Nov 18 13:45:47 2019 -0500
@@ -11,7 +11,7 @@
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
 ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2  --tumor-sample SRR8525881 --output output.vcf --interval-set-rule UNION --interval-exclusion-padding 0 --input input.bam --read-validation-stringency SILENT --reference reference.fa --add-output-sam-program-record true --add-output-vcf-command-line true --verbosity ERROR --QUIET true --read-filter AmbiguousBaseReadFilter --read-filter FirstOfPairReadFilter --read-filter GoodCigarReadFilter  --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --dont-trim-active-regions false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --interval-padding 0 --interval-merging-rule ALL --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --ambig-filter-frac 0.05 --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.4.0",Date="October 29, 2019 1:14:20 PM EDT">
+##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2  --tumor-sample SRR8525881 --output output.vcf --input input.bam --reference reference.fa --QUIET true  --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --dont-trim-active-regions false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.4.0",Date="November 15, 2019 4:25:08 PM EST">
 ##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination">
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
 ##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype">
@@ -41,44 +41,53 @@
 ##source=Mutect2
 ##tumor_sample=SRR8525881
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SRR8525881
-K03455	4861	.	A	G	.	.	DP=1;ECNT=14;MBQ=0,37;MFRL=0,400;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=4.20	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:0,1:0.667:1:0,1:0,0:0,0,1,0
-K03455	4918	.	G	A	.	.	DP=7;ECNT=14;MBQ=38,37;MFRL=303,370;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=8.65	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:3,3:0.499:6:2,0:1,2:2,1,0,3
-K03455	4923	.	A	G	.	.	DP=8;ECNT=14;MBQ=0,33;MFRL=0,314;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=34.22	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:0,8:0.900:8:0,3:0,3:0,0,3,5
-K03455	4949	.	G	A	.	.	DP=12;ECNT=14;MBQ=38,37;MFRL=285,264;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=27.49	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:5,7:0.573:12:2,2:1,4:0|1:4949_G_A:4949:2,3,2,5
-K03455	4952	.	C	T	.	.	DP=13;ECNT=14;MBQ=36,37;MFRL=285,264;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=27.48	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:5,7:0.573:12:1,2:2,5:0|1:4949_G_A:4949:2,3,2,5
-K03455	4988	.	T	C	.	.	DP=22;ECNT=14;MBQ=36,38;MFRL=285,278;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=14.99	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:17,5:0.250:22:5,2:8,2:6,11,3,2
-K03455	4991	.	T	C	.	.	DP=22;ECNT=14;MBQ=37,28;MFRL=271,309;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=4.85	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:20,2:0.125:22:8,0:10,1:9,11,0,2
-K03455	4996	.	AC	GA	.	.	DP=25;ECNT=14;MBQ=38,32;MFRL=285,203;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=5.72	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:21,3:0.152:24:6,1:10,1:8,13,1,2
-K03455	4997	.	C	T,A	.	.	DP=25;ECNT=14;MBQ=38,37,38;MFRL=282,292,264;MMQ=60,60,60;MPOS=10,31;POPAF=7.30,7.30;TLOD=8.86,34.99	GT:AD:AF:DP:F1R2:F2R1:SB	0/1/2:8,3,13:0.148,0.517:24:4,0,5:3,2,8:5,3,5,11
-K03455	5004	.	G	A	.	.	DP=26;ECNT=14;MBQ=37,36;MFRL=262,288;MMQ=60,60;MPOS=51;POPAF=7.30;TLOD=4.21	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:24,2:0.107:26:7,1:13,1:8,16,1,1
-K03455	5015	.	A	G	.	.	DP=34;ECNT=14;MBQ=38,38;MFRL=269,258;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=88.69	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:10,22:0.677:32:4,5:6,16:4,6,5,17
-K03455	5018	.	A	G	.	.	DP=34;ECNT=14;MBQ=38,38;MFRL=262,261;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=11.32	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:30,4:0.139:34:9,0:15,4:10,20,0,4
-K03455	5027	.	G	A	.	.	DP=37;ECNT=14;MBQ=37,38;MFRL=260,229;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=12.64	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:31,5:0.157:36:10,0:18,5:0|1:5027_G_A:5027:10,21,0,5
-K03455	5036	.	G	A	.	.	DP=36;ECNT=14;MBQ=39,38;MFRL=256,229;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=12.71	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:30,5:0.162:35:9,0:18,4:0|1:5027_G_A:5027:10,20,0,5
-K03455	5076	.	A	G	.	.	DP=37;ECNT=27;MBQ=38,37;MFRL=278,190;MMQ=60,60;MPOS=54;POPAF=7.30;TLOD=15.35	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:31,5:0.158:36:5,0:25,5:0|1:5076_A_G:5076:5,26,0,5
-K03455	5098	.	A	G	.	.	DP=42;ECNT=27;MBQ=38,38;MFRL=190,292;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=126.26	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:7,32:0.804:39:0,4:7,22:0,7,4,28
-K03455	5099	.	C	T	.	.	DP=42;ECNT=27;MBQ=38,37;MFRL=292,190;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=22.52	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:34,7:0.186:41:4,0:28,6:0|1:5076_A_G:5076:4,30,0,7
-K03455	5121	.	C	T	.	.	DP=41;ECNT=27;MBQ=37,38;MFRL=257,205;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=24.97	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:33,8:0.209:41:3,1:28,6:3,30,1,7
-K03455	5130	.	TG	CA	.	.	DP=38;ECNT=27;MBQ=38,38;MFRL=194,275;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=122.82	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:8,30:0.778:38:0,0:7,28:0,8,2,28
-K03455	5131	.	G	A	.	.	DP=38;ECNT=27;MBQ=0,38;MFRL=0,205;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=23.77	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:0,8:0.932:8:0,1:0,6:0,0,1,7
-K03455	5133	.	T	C	.	.	DP=36;ECNT=27;MBQ=38,36;MFRL=293,216;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=31.26	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:27,9:0.268:36:2,0:23,8:0|1:5133_T_C:5133:2,25,0,9
-K03455	5137	.	GG	AG,AA	.	.	DP=35;ECNT=27;MBQ=39,39,39;MFRL=194,216,337;MMQ=60,60,60;MPOS=34,28;POPAF=7.30,7.30;TLOD=31.44,66.06	GT:AD:AF:DP:F1R2:F2R1:SB	0/1/2:8,9,18:0.270,0.495:35:0,0,1:7,8,16:0,8,1,26
-K03455	5146	.	AGG	A	.	.	DP=33;ECNT=27;MBQ=38,38;MFRL=315,216;MMQ=60,60;MPOS=43;POPAF=7.30;RPA=4,2;RU=G;STR;TLOD=31.38	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:24,9:0.286:33:1,0:22,9:0|1:5133_T_C:5133:1,23,0,9
-K03455	5147	.	G	A	.	.	DP=33;ECNT=27;MBQ=38,37;MFRL=181,343;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=66.04	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:7,17:0.694:24:0,0:6,13:0|1:5147_G_A:5147:0,7,1,16
-K03455	5153	.	GGTTT	G	.	.	DP=29;ECNT=27;MBQ=38,38;MFRL=296,216;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=32.02	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:20,9:0.323:29:0,0:19,9:0|1:5133_T_C:5133:0,20,0,9
-K03455	5155	.	T	C	.	.	DP=28;ECNT=27;MBQ=38,38;MFRL=169,331;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=49.64	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:6,13:0.669:19:0,0:6,12:0|1:5147_G_A:5147:0,6,0,13
-K03455	5156	.	T	A	.	.	DP=28;ECNT=27;MBQ=38,37;MFRL=315,181;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=16.29	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:14,5:0.283:19:0,0:14,5:0|1:5156_T_A:5156:0,14,0,5
-K03455	5157	.	T	G	.	.	DP=28;ECNT=27;MBQ=38,37;MFRL=181,331;MMQ=60,60;MPOS=54;POPAF=7.30;TLOD=49.65	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:5,13:0.703:18:0,0:5,13:0,5,0,13
-K03455	5169	.	C	T	.	.	DP=20;ECNT=27;MBQ=39,39;MFRL=296,170;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=20.02	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:14,6:0.318:20:0,0:14,6:0,14,0,6
-K03455	5175	.	A	T	.	.	DP=19;ECNT=27;MBQ=37,39;MFRL=203,299;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=34.23	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:10,9:0.476:19:0,0:9,9:0|1:5147_G_A:5147:0,10,0,9
-K03455	5177	.	G	C	.	.	DP=18;ECNT=27;MBQ=39,37;MFRL=299,216;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=25.72	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:11,7:0.400:18:0,0:10,7:0|1:5133_T_C:5133:0,11,0,7
-K03455	5179	.	CC	AC,AA	.	.	DP=17;ECNT=27;MBQ=39,36,39;MFRL=366,216,315;MMQ=60,60,60;MPOS=60,51;POPAF=7.30,7.30;TLOD=26.12,30.50	GT:AD:AF:DP:F1R2:F2R1:SB	0/1/2:2,7,8:0.400,0.450:17:0,0,0:2,7,8:0,2,0,15
-K03455	5189	.	G	A	.	.	DP=18;ECNT=27;MBQ=39,39;MFRL=203,315;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=30.08	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:10,8:0.450:18:1,0:9,8:1,9,0,8
-K03455	5190	.	A	G	.	.	DP=18;ECNT=27;MBQ=39,20;MFRL=293,181;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=9.31	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:15,3:0.200:18:0,0:15,2:0|1:5156_T_A:5156:0,15,1,2
-K03455	5196	.	T	C	.	.	DP=18;ECNT=27;MBQ=39,37;MFRL=293,181;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=9.19	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:15,3:0.200:18:0,1:15,2:0,15,1,2
-K03455	5220	.	G	A	.	.	DP=16;ECNT=27;MBQ=38,38;MFRL=312,219;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=21.54	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:10,6:0.389:16:1,0:9,6:0|1:5220_G_A:5220:1,9,0,6
-K03455	5223	.	T	A	.	.	DP=16;ECNT=27;MBQ=37,39;MFRL=293,181;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=9.40	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:13,3:0.222:16:0,1:13,2:0|1:5223_T_A:5223:0,13,1,2
-K03455	5230	.	T	C	.	.	DP=16;ECNT=27;MBQ=38,39;MFRL=293,181;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=9.40	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:13,3:0.222:16:0,1:12,2:0|1:5223_T_A:5223:0,13,1,2
-K03455	5233	.	G	A	.	.	DP=12;ECNT=27;MBQ=38,38;MFRL=293,216;MMQ=60,60;MPOS=11;POPAF=7.30;TLOD=18.49	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:7,5:0.429:12:0,0:6,5:0|1:5220_G_A:5220:1,6,0,5
-K03455	5236	.	A	G	.	.	DP=12;ECNT=27;MBQ=37,38;MFRL=216,256;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=22.57	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:5,6:0.539:11:0,1:5,5:0,5,1,5
-K03455	5240	.	C	T	.	.	DP=11;ECNT=27;MBQ=37,37;MFRL=219,162;MMQ=60,60;MPOS=-1;POPAF=7.30;TLOD=9.66	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:8,3:0.308:11:0,0:7,3:1,7,0,3
+K03455	4861	.	A	G	.	.	DP=1;ECNT=13;MBQ=0,37;MFRL=0,400;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=3.88	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:0,1:0.667:1:0,1:0,0:0,0,1,0
+K03455	4918	.	G	A	.	.	DP=10;ECNT=13;MBQ=37,32;MFRL=282,328;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=17.51	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:4,6:0.583:10:2,1:2,3:3,1,1,5
+K03455	4923	.	A	G	.	.	DP=11;ECNT=13;MBQ=0,33;MFRL=0,303;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=50.89	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:0,11:0.923:11:0,4:0,5:0,0,5,6
+K03455	4949	.	G	A	.	.	DP=16;ECNT=13;MBQ=38,37;MFRL=281,279;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=40.32	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:6,10:0.647:16:2,3:2,6:0|1:4949_G_A:4949:3,3,4,6
+K03455	4952	.	C	T	.	.	DP=18;ECNT=13;MBQ=25,37;MFRL=281,279;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=40.30	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:6,10:0.647:16:2,3:2,7:0|1:4949_G_A:4949:3,3,4,6
+K03455	4988	.	T	C	.	.	DP=32;ECNT=13;MBQ=34,35;MFRL=261,290;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=23.96	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:24,8:0.258:32:9,4:12,3:12,12,4,4
+K03455	4991	.	T	C	.	.	DP=32;ECNT=13;MBQ=33,20;MFRL=264,292;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=6.07	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:29,3:0.128:32:13,1:15,1:15,14,1,2
+K03455	4996	.	AC	GA	.	.	DP=36;ECNT=13;MBQ=37,26;MFRL=264,256;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=11.76	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:29,6:0.181:35:10,2:12,3:14,15,3,3
+K03455	4997	.	C	T,A	.	.	DP=36;ECNT=13;MBQ=20,20,38;MFRL=278,131,257;MMQ=60,60,60;MPOS=10,31;POPAF=7.30,7.30;TLOD=14.89,42.60	GT:AD:AF:DP:F1R2:F2R1:SB	0/1/2:11,5,19:0.149,0.553:35:6,1,7:3,3,12:6,5,11,13
+K03455	5015	.	A	G	.	.	DP=49;ECNT=13;MBQ=27,37;MFRL=245,251;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=126.23	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:14,32:0.721:46:7,8:6,23:6,8,14,18
+K03455	5018	.	A	G	.	.	DP=49;ECNT=13;MBQ=33,20;MFRL=257,180;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=14.66	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:43,6:0.129:49:13,1:21,5:19,24,2,4
+K03455	5027	.	G	A	.	.	DP=54;ECNT=13;MBQ=33,20;MFRL=254,158;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=16.84	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:46,7:0.148:53:15,1:25,6:0|1:5027_G_A:5027:19,27,2,5
+K03455	5036	.	G	A	.	.	DP=53;ECNT=13;MBQ=32,20;MFRL=251,158;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=16.91	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:45,7:0.151:52:17,1:25,5:0|1:5027_G_A:5027:19,26,2,5
+K03455	5076	.	A	G	.	.	DP=49;ECNT=29;MBQ=36,20;MFRL=260,210;MMQ=60,60;MPOS=54;POPAF=7.30;TLOD=15.53	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:43,6:0.151:49:12,1:28,5:0|1:5076_A_G:5076:11,32,0,6
+K03455	5098	.	A	G	.	.	DP=55;ECNT=29;MBQ=20,32;MFRL=210,269;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=180.82	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:8,46:0.816:54:0,9:7,26:0,8,10,36
+K03455	5099	.	C	T	.	.	DP=55;ECNT=29;MBQ=33,20;MFRL=269,210;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=22.21	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:46,8:0.183:54:8,1:31,6:0|1:5076_A_G:5076:10,36,0,8
+K03455	5121	.	C	T	.	.	DP=55;ECNT=29;MBQ=20,20;MFRL=251,245;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=54.15	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:39,16:0.265:55:7,5:30,9:6,33,4,12
+K03455	5130	.	TG	CA	.	.	DP=49;ECNT=29;MBQ=20,37;MFRL=205,251;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=145.65	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:14,35:0.739:49:4,4:8,29:3,11,3,32
+K03455	5131	.	G	A	.	.	DP=49;ECNT=29;MBQ=0,20;MFRL=0,205;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=53.22	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:0,14:0.951:14:0,3:0,9:0,0,3,11
+K03455	5133	.	T	C	.	.	DP=46;ECNT=29;MBQ=35,36;MFRL=285,219;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=31.79	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:36,10:0.251:46:6,1:26,8:0|1:5133_T_C:5133:5,31,0,10
+K03455	5137	.	GG	AG,AA	.	.	DP=45;ECNT=29;MBQ=26,39,39;MFRL=205,219,309;MMQ=60,60,60;MPOS=36,37;POPAF=7.30,7.30;TLOD=32.04,80.27	GT:AD:AF:DP:F1R2:F2R1:SB	0/1/2:14,10,21:0.246,0.487:45:4,1,3:9,8,16:3,11,1,30
+K03455	5146	.	AGG	A	.	.	DP=43;ECNT=29;MBQ=38,37;MFRL=278,219;MMQ=60,60;MPOS=45;POPAF=7.30;RPA=4,2;RU=G;STR;TLOD=32.02	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:33,10:0.261:43:6,1:24,9:0|1:5133_T_C:5133:4,29,0,10
+K03455	5147	.	G	A	.	.	DP=43;ECNT=29;MBQ=20,38;MFRL=205,331;MMQ=60,60;MPOS=46;POPAF=7.30;TLOD=75.96	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:14,19:0.626:33:4,2:9,13:0|1:5147_G_A:5147:3,11,1,18
+K03455	5149	.	G	A	.	.	DP=42;ECNT=29;MBQ=37,18;MFRL=254,64;MMQ=60,60;MPOS=13;POPAF=7.30;TLOD=4.70	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:40,2:0.049:42:6,0:28,1:3,37,1,1
+K03455	5153	.	GGTTT	G	.	.	DP=40;ECNT=29;MBQ=34,37;MFRL=269,219;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=32.44	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:30,10:0.281:40:6,1:22,9:0|1:5133_T_C:5133:3,27,0,10
+K03455	5155	.	T	C	.	.	DP=39;ECNT=29;MBQ=20,38;MFRL=181,315;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=63.73	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:13,16:0.608:29:4,2:8,13:0|1:5147_G_A:5147:3,10,0,16
+K03455	5156	.	T	A	.	.	DP=39;ECNT=29;MBQ=37,33;MFRL=296,260;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=39.44	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:18,11:0.356:29:2,4:16,7:0|1:5156_T_A:5156:1,17,2,9
+K03455	5157	.	T	G,C	.	.	DP=39;ECNT=29;MBQ=20,37,20;MFRL=260,315,64;MMQ=60,60,60;MPOS=56,5;POPAF=7.30,7.30;TLOD=63.79,5.70	GT:AD:AF:DP:F1R2:F2R1:SB	0/1/2:11,16,2:0.591,0.064:29:4,2,0:7,14,2:2,9,1,17
+K03455	5169	.	C	T	.	.	DP=29;ECNT=29;MBQ=38,32;MFRL=275,190;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=39.25	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:18,11:0.379:29:2,4:15,7:1,17,1,10
+K03455	5175	.	A	T	.	.	DP=26;ECNT=29;MBQ=36,38;MFRL=222,293;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=52.80	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:13,13:0.481:26:3,2:9,11:0|1:5147_G_A:5147:0,13,1,12
+K03455	5177	.	G	C	.	.	DP=25;ECNT=29;MBQ=37,37;MFRL=293,219;MMQ=60,60;MPOS=58;POPAF=7.30;TLOD=28.74	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:17,8:0.346:25:4,1:12,7:0|1:5133_T_C:5133:1,16,0,8
+K03455	5179	.	CC	AC,AA	.	.	DP=24;ECNT=29;MBQ=38,34,38;MFRL=339,219,296;MMQ=60,60,60;MPOS=58,51;POPAF=7.30,7.30;TLOD=29.12,49.40	GT:AD:AF:DP:F1R2:F2R1:SB	0/1/2:4,8,12:0.346,0.462:24:2,1,2:2,7,10:0,4,1,19
+K03455	5189	.	G	A	.	.	DP=25;ECNT=29;MBQ=39,39;MFRL=222,296;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=48.64	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:13,12:0.462:25:4,2:9,10:1,12,1,11
+K03455	5190	.	A	G	.	.	DP=25;ECNT=29;MBQ=39,20;MFRL=252,278;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=15.35	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:20,5:0.231:25:3,2:17,2:0|1:5156_T_A:5156:1,19,1,4
+K03455	5196	.	T	C	.	.	DP=25;ECNT=29;MBQ=38,20;MFRL=246,339;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=6.08	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:21,4:0.191:25:3,3:18,1:1,20,1,3
+K03455	5220	.	G	A	.	.	DP=23;ECNT=29;MBQ=37,37;MFRL=286,222;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=24.08	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:16,7:0.344:23:5,1:11,6:0|1:5220_G_A:5220:2,14,0,7
+K03455	5223	.	T	A	.	.	DP=22;ECNT=29;MBQ=37,37;MFRL=257,278;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=17.15	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:17,5:0.269:22:2,3:14,2:0|1:5223_T_A:5223:1,16,1,4
+K03455	5226	.	T	C	.	.	DP=22;ECNT=29;MBQ=34,35;MFRL=268,253;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=12.23	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:16,6:0.231:22:4,1:12,5:1,15,1,5
+K03455	5230	.	T	C	.	.	DP=21;ECNT=29;MBQ=33,38;MFRL=275,278;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=17.08	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:16,5:0.281:21:2,3:13,2:0|1:5223_T_A:5223:1,15,1,4
+K03455	5233	.	G	A	.	.	DP=16;ECNT=29;MBQ=38,38;MFRL=293,216;MMQ=60,60;MPOS=11;POPAF=7.30;TLOD=17.95	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:11,5:0.369:16:3,0:7,5:0|1:5220_G_A:5220:2,9,0,5
+K03455	5236	.	A	G	.	.	DP=16;ECNT=29;MBQ=37,38;MFRL=216,293;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=40.42	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:5,11:0.631:16:0,4:5,6:0,5,2,9
+K03455	5240	.	C	T	.	.	DP=15;ECNT=29;MBQ=37,37;MFRL=250,162;MMQ=60,60;MPOS=-1;POPAF=7.30;TLOD=9.14	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:12,3:0.250:15:3,0:8,3:2,10,0,3
+K03455	6902	.	A	C	.	.	DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=65;POPAF=7.30;TLOD=4.20	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1
+K03455	6905	.	A	G	.	.	DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=4.20	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1
+K03455	6911	.	T	C	.	.	DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=4.20	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1
+K03455	6917	.	G	A	.	.	DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=4.20	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1
+K03455	6920	.	G	A	.	.	DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=47;POPAF=7.30;TLOD=4.20	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1
+K03455	6923	.	C	T	.	.	DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=4.20	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1
+K03455	6931	.	C	A	.	.	DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=4.20	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1
+K03455	6936	.	C	G	.	.	DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=4.20	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1
diff -r f41a1e03538b -r fd2d6e035c3f test-data/Mutect2-out3.vcf
--- a/test-data/Mutect2-out3.vcf	Wed Oct 30 15:33:59 2019 -0400
+++ b/test-data/Mutect2-out3.vcf	Mon Nov 18 13:45:47 2019 -0500
@@ -11,7 +11,7 @@
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
 ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2  --tumor-sample SRR8525881 --af-of-alleles-not-in-resource -1.0 --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --max-population-af 0.01 --downsampling-stride 1 --normal-lod 2.2 --base-quality-score-threshold 18 --native-pair-hmm-threads 1 --min-base-quality-score 10 --output output.vcf --max-reads-per-alignment-start 50 --interval-padding 0 --interval-merging-rule ALL --input input.bam --reference reference.fa --QUIET true --gcs-max-retries 20 --annotation StrandBiasBySample --annotation BaseQualityHistogram --annotation OrientationBiasReadCounts --annotation-group StandardMutectAnnotation  --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --mitochondria-mode false --pcr-snv-qual 40 --pcr-indel-qual 40 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --dont-trim-active-regions false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --interval-set-rule UNION --interval-exclusion-padding 0 --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.4.0",Date="October 29, 2019 1:15:01 PM EDT">
+##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2  --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --tumor-sample SRR8525881 --af-of-alleles-not-in-resource -1.0 --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --normal-lod 2.2 --base-quality-score-threshold 18 --native-pair-hmm-threads 1 --min-base-quality-score 10 --output output.vcf --max-reads-per-alignment-start 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --input input.bam --read-validation-stringency SILENT --reference reference.fa --add-output-sam-program-record true --add-output-vcf-command-line true --verbosity ERROR --QUIET true --gcs-max-retries 20 --annotation StrandBiasBySample --annotation BaseQualityHistogram --annotation OrientationBiasReadCounts --annotation-group StandardMutectAnnotation  --genotype-pon-sites false --genotype-germline-sites false --mitochondria-mode false --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --dont-trim-active-regions false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --use-jdk-deflater false --use-jdk-inflater false --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.4.0",Date="November 15, 2019 4:25:49 PM EST">
 ##INFO=<ID=BQHIST,Number=A,Type=Integer,Description="Base quality counts for each allele represented sparsely as alternating entries of qualities and counts for each allele.For example [10,1,0,20,0,1] means one ref base with quality 10 and one alt base with quality 20.">
 ##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination">
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
diff -r f41a1e03538b -r fd2d6e035c3f test-data/Mutect2-out4.vcf
--- a/test-data/Mutect2-out4.vcf	Wed Oct 30 15:33:59 2019 -0400
+++ b/test-data/Mutect2-out4.vcf	Mon Nov 18 13:45:47 2019 -0500
@@ -11,7 +11,7 @@
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
 ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2  --tumor-sample SRR8525881 --af-of-alleles-not-in-resource -1.0 --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --max-population-af 0.01 --downsampling-stride 1 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --dont-trim-active-regions true --num-pruning-samples 1 --min-dangling-branch-length 4 --max-num-haplotypes-in-population 128 --min-pruning 2 --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 1 --bam-writer-type CALLED_HAPLOTYPES --min-base-quality-score 10 --smith-waterman FASTEST_AVAILABLE --max-mnp-distance 1 --output output.vcf --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --interval-padding 0 --interval-merging-rule ALL --input input.bam --reference reference.fa --QUIET true --gcs-max-retries 20  --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --mitochondria-mode false --pcr-snv-qual 40 --pcr-indel-qual 40 --callable-depth 10 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --recover-all-dangling-branches false --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --native-pair-hmm-use-double-precision false --dont-use-soft-clipped-bases false --emit-ref-confidence NONE --force-call-filtered-alleles false --force-active false --interval-set-rule UNION --interval-exclusion-padding 0 --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.4.0",Date="October 29, 2019 1:15:43 PM EDT">
+##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2  --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --tumor-sample SRR8525881 --af-of-alleles-not-in-resource -1.0 --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --minimum-allele-fraction 0.0 --dont-trim-active-regions true --num-pruning-samples 1 --min-dangling-branch-length 4 --max-num-haplotypes-in-population 128 --min-pruning 2 --pruning-lod-threshold 2.30258509299 --max-unpruned-variants 100 --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 1 --bam-writer-type CALLED_HAPLOTYPES --min-base-quality-score 10 --smith-waterman FASTEST_AVAILABLE --emit-ref-confidence NONE --max-mnp-distance 1 --output output.vcf --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --input input.bam --read-validation-stringency SILENT --reference reference.fa --add-output-sam-program-record true --add-output-vcf-command-line true --verbosity ERROR --QUIET true --gcs-max-retries 20  --genotype-pon-sites false --genotype-germline-sites false --mitochondria-mode false --callable-depth 10 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --independent-mates false --disable-adaptive-pruning false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --recover-all-dangling-branches false --adaptive-pruning-initial-error-rate 0.001 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --native-pair-hmm-use-double-precision false --dont-use-soft-clipped-bases false --force-call-filtered-alleles false --force-active false --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --use-jdk-deflater false --use-jdk-inflater false --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.4.0",Date="November 15, 2019 4:26:31 PM EST">
 ##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination">
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
 ##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype">
diff -r f41a1e03538b -r fd2d6e035c3f test-data/Mutect2-out5.vcf
--- a/test-data/Mutect2-out5.vcf	Wed Oct 30 15:33:59 2019 -0400
+++ b/test-data/Mutect2-out5.vcf	Mon Nov 18 13:45:47 2019 -0500
@@ -11,7 +11,7 @@
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
 ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2  --tumor-sample SRR8525881 --bam-output debug.bam --output output.vcf --activity-profile-out activity-profile.tab --assembly-region-out assembly-region.tab --input input.bam --reference reference.fa --QUIET true  --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --dont-trim-active-regions false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.4.0",Date="October 29, 2019 2:55:53 PM EDT">
+##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2  --tumor-sample SRR8525881 --bam-output debug.bam --output output.vcf --activity-profile-out activity-profile.tab --assembly-region-out assembly-region.tab --input input.bam --reference reference.fa --QUIET true  --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --dont-trim-active-regions false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.4.0",Date="November 15, 2019 4:26:58 PM EST">
 ##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination">
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
 ##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype">