Mercurial > repos > nml > filter_vcf

annotate test-data/filterVcf.input.1.vcf @ 0:93ea196681c8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
author nml
date Tue, 27 Aug 2019 12:31:30 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
1 ##fileformat=VCFv4.1
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
2 ##fileDate=20140423
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
3 ##source=freeBayes version 0.9.8
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
4 ##reference=/home/aaron/microbialinformatics2014/core-snv-tutorial/output-10-subsample/reference/2010EL-1749.2010EL-1786-c1_2000_2400kb.fasta
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
5 ##phasing=none
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
6 ##commandline="/opt/freebayes/freebayes --bam /home/aaron/microbialinformatics2014/core-snv-tutorial/output-10-subsample/bam/2010EL-1749.bam --vcf /home/aaron/microbialinformatics2014/core-snv-tutorial/output-10-subsample/vcf/2010EL-1749.vcf --fasta-reference /home/aaron/microbialinformatics2014/core-snv-tutorial/output-10-subsample/reference/2010EL-1749.2010EL-1786-c1_2000_2400kb.fasta --min-coverage 2 --pvar 0 --ploidy 1 --left-align-indels --min-mapping-quality 30 --min-base-quality 30 --min-alternate-fraction 0.75"
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
7 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
8 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
9 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
10 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
11 ##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
12 ##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observations">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
13 ##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
14 ##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
15 ##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
16 ##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
17 ##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
18 ##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
19 ##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
20 ##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
21 ##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
22 ##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
23 ##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without.">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
24 ##INFO=<ID=XRM,Number=1,Type=Float,Description="Reference allele read mismatch rate: The rate of SNVs + MNPs + INDELs in reads supporting the reference allele.">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
25 ##INFO=<ID=XRS,Number=1,Type=Float,Description="Reference allele read SNV rate: The rate of per-base mismatches (SNVs + MNPs) in reads supporting the reference allele.">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
26 ##INFO=<ID=XRI,Number=1,Type=Float,Description="Reference allele read INDEL rate: The rate of INDELs (gaps) in reads supporting the reference allele.">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
27 ##INFO=<ID=XAM,Number=A,Type=Float,Description="Alternate allele read mismatch rate: The rate of SNVs + MNPs + INDELs in reads supporting the alternate allele, excluding the called variant.">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
28 ##INFO=<ID=XAS,Number=A,Type=Float,Description="Alternate allele read SNV rate: The rate of per-base mismatches (SNVs + MNPs) in reads supporting the alternate allele, excluding the called variant.">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
29 ##INFO=<ID=XAI,Number=A,Type=Float,Description="Alternate allele read INDEL rate: The rate of INDELs (gaps) in reads supporting the alternate allele, excluding the called variant.">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
30 ##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
31 ##INFO=<ID=BVAR,Number=0,Type=Flag,Description="The best genotype combination in the posterior is variant (non homozygous).">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
32 ##INFO=<ID=CpG,Number=0,Type=Flag,Description="CpG site (either CpG, TpG or CpA)">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
33 ##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snv, mnp, ins, del, or complex.">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
34 ##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
35 ##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
36 ##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
37 ##INFO=<ID=HWE,Number=1,Type=Float,Description="Phred-scaled discrete HWE prior probability of the genotyping across all samples.">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
38 ##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
39 ##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
40 ##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
41 ##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
42 ##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
43 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
44 ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
45 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
46 ##FORMAT=<ID=GLE,Number=1,Type=String,Description="Genotype Likelihood Explicit, same as GL, but with tags to indicate the specific genotype. For instance, 0^-75.22|1^-223.42|0/0^-323.03|1/0^-99.29|1/1^-802.53 represents both haploid and diploid genotype likilehoods in a biallelic context">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
47 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
48 ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
49 ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
50 ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
51 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
52 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
53 gi|360034408|ref|NC_016445.1|_2000000_2400000 128 . GA AT 197.867 . AB=0;ABP=0;AC=1;AF=1;AN=1;AO=3;CIGAR=1X;DP=3;DPRA=0;EPP=3.73412;EPPR=0;HWE=-0;LEN=1;MEANALT=1;MQM=54;MQMR=0;NS=1;NUMALT=1;ODDS=45.5605;PAIRED=0;PAIREDR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAP=3.73412;SRP=0;TYPE=snv;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1:50000:3:0:0:3:212:-19.7867,0
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
54 gi|360034408|ref|NC_016445.1|_2000000_2400000 256 . A C 250.1 . AB=0;ABP=0;AC=1;AF=1;AN=1;AO=6;CIGAR=1X;DP=8;DPRA=0;EPP=8.80089;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=54;MQMR=54;NS=1;NUMALT=1;ODDS=57.5877;PAIRED=0;PAIREDR=0;RO=2;RPP=8.80089;RPPR=7.35324;RUN=1;SAP=4.45795;SRP=3.0103;TYPE=snv;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1:50000:8:2:142:6:420:-38.5,-13.49
93ea196681c8 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
nml
parents:
diff changeset
55 gi|360034408|ref|NC_016445.1|_2000000_2400000 512 . AT C 250.1 . AB=0;ABP=0;AC=1;AF=1;AN=1;AO=6;CIGAR=1X;DP=8;DPRA=0;EPP=8.80089;EPPR=3.0103;HWE=-0;LEN=1;MEANALT=1;MQM=54;MQMR=54;NS=1;NUMALT=1;ODDS=57.5877;PAIRED=0;PAIREDR=0;RO=2;RPP=8.80089;RPPR=7.35324;RUN=1;SAP=4.45795;SRP=3.0103;TYPE=snv;XAI=0;XAM=0;XAS=0;XRI=0;XRM=0;XRS=0;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1:50000:8:2:142:6:420:-38.5,-13.49