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comparison test-data/freebayes-phix174-test2.vcf @ 27:9f164587a92f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
author iuc
date Tue, 06 Jun 2017 11:44:38 -0400
parents 52aed7d9ed2b
children ef2c525bd8cd
comparison
equal deleted inserted replaced
26:a028d13cd860 27:9f164587a92f
1 ##fileformat=VCFv4.1 1 ##fileformat=VCFv4.2
2 ##reference=localref.fa 2 ##reference=localref.fa
3 ##contig=<ID=phiX174,length=5386> 3 ##contig=<ID=phiX174,length=5386>
4 ##phasing=none 4 ##phasing=none
5 ##commandline="freebayes --region phiX174:0..5386 --bam b_0.bam --fasta-reference localref.fa --vcf ./vcf_output/part_phiX174:0..5386.vcf --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --report-monomorphic --standard-filters --min-coverage 14" 5 ##commandline="freebayes --region phiX174:0..5386 --bam b_0.bam --fasta-reference localref.fa --vcf ./vcf_output/part_phiX174:0..5386.vcf --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --report-monomorphic --standard-filters --min-coverage 14"
6 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> 6 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
7 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> 7 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
8 ##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> 8 ##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
9 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> 9 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
10 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> 10 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
11 ##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]"> 11 ##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
12 ##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally"> 12 ##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
13 ##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally"> 13 ##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
14 ##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally"> 14 ##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
15 ##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally"> 15 ##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
16 ##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> 16 ##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
17 ##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> 17 ##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
18 ##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations"> 18 ##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
48 ##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record."> 48 ##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record.">
49 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 49 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
50 ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype"> 50 ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
51 ##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"> 51 ##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">
52 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> 52 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
53 ##FORMAT=<ID=DPR,Number=A,Type=Integer,Description="Number of observation for each allele"> 53 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele">
54 ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> 54 ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
55 ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> 55 ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
56 ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> 56 ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
57 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> 57 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
58 ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> 58 ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
59 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown 59 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown
60 phiX174 1134 . A . 0 . DP=14;DPB=14;EPPR=3.0103;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=916;RO=14;RPPR=8.59409 GT:DP:DPR:RO:QR:AO:QA:GL 0/0:14:14:14:916:.:.:0 60 phiX174 1134 . A . 0 . DP=14;DPB=14;EPPR=3.0103;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=916;RO=14;RPPR=8.59409 GT:DP:AD:RO:QR:AO:QA:GL 0/0:14:14:14:916:.:.:0
61 phiX174 1135 . C . 0 . DP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=957;RO=14;RPPR=5.49198 GT:DP:DPR:RO:QR:AO:QA:GL 0/0:14:14:14:957:.:.:0 61 phiX174 1135 . C . 0 . DP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=957;RO=14;RPPR=5.49198 GT:DP:AD:RO:QR:AO:QA:GL 0/0:14:14:14:957:.:.:0
62 phiX174 1136 . G . 0 . DP=14;DPB=14;EPPR=8.59409;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=919;RO=14;RPPR=3.0103 GT:DP:DPR:RO:QR:AO:QA:GL 0/0:14:14:14:919:.:.:0 62 phiX174 1136 . G . 0 . DP=14;DPB=14;EPPR=8.59409;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=919;RO=14;RPPR=3.0103 GT:DP:AD:RO:QR:AO:QA:GL 0/0:14:14:14:919:.:.:0
63 phiX174 1137 . C . 0 . DP=14;DPB=14;EPPR=5.49198;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=927;RO=14;RPPR=3.63072 GT:DP:DPR:RO:QR:AO:QA:GL 0/0:14:14:14:927:.:.:0 63 phiX174 1137 . C . 0 . DP=14;DPB=14;EPPR=5.49198;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=927;RO=14;RPPR=3.63072 GT:DP:AD:RO:QR:AO:QA:GL 0/0:14:14:14:927:.:.:0
64 phiX174 1138 . C . 0 . DP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=876;RO=14;RPPR=5.49198 GT:DP:DPR:RO:QR:AO:QA:GL 0/0:14:14:14:876:.:.:0 64 phiX174 1138 . C . 0 . DP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=876;RO=14;RPPR=5.49198 GT:DP:AD:RO:QR:AO:QA:GL 0/0:14:14:14:876:.:.:0
65 phiX174 1139 . G . 0 . DP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=946;RO=14;RPPR=5.49198 GT:DP:DPR:RO:QR:AO:QA:GL 0/0:14:14:14:946:.:.:0 65 phiX174 1139 . G . 0 . DP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=946;RO=14;RPPR=5.49198 GT:DP:AD:RO:QR:AO:QA:GL 0/0:14:14:14:946:.:.:0
66 phiX174 1140 . T . 0 . DP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=927;RO=15;RPPR=4.31318 GT:DP:DPR:RO:QR:AO:QA:GL 0/0:15:15:15:927:.:.:0 66 phiX174 1140 . T . 0 . DP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=927;RO=15;RPPR=4.31318 GT:DP:AD:RO:QR:AO:QA:GL 0/0:15:15:15:927:.:.:0
67 phiX174 1141 . T G 3.61953e-07 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=3.63072;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=37;NS=1;NUMALT=1;ODDS=16.3003;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=50;QR=880;RO=14;RPL=0;RPP=5.18177;RPPR=5.49198;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=5.49198;SRR=9;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 0/0:15:15,1:14:880:1:50:0,-0.836684,-42.5367 67 phiX174 1141 . T G 3.61953e-07 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=3.63072;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=37;NS=1;NUMALT=1;ODDS=16.3003;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=50;QR=880;RO=14;RPL=0;RPP=5.18177;RPPR=5.49198;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=5.49198;SRR=9;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/0:15:14,1:14:880:1:50:0,-0.836684,-42.5367
68 phiX174 1142 . G . 0 . DP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1082;RO=16;RPPR=3.55317 GT:DP:DPR:RO:QR:AO:QA:GL 0/0:16:16:16:1082:.:.:0 68 phiX174 1142 . G . 0 . DP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1082;RO=16;RPPR=3.55317 GT:DP:AD:RO:QR:AO:QA:GL 0/0:16:16:16:1082:.:.:0
69 phiX174 1143 . G . 0 . DP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1029;RO=16;RPPR=3.55317 GT:DP:DPR:RO:QR:AO:QA:GL 0/0:16:16:16:1029:.:.:0 69 phiX174 1143 . G . 0 . DP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1029;RO=16;RPPR=3.55317 GT:DP:AD:RO:QR:AO:QA:GL 0/0:16:16:16:1029:.:.:0
70 phiX174 1144 . C . 0 . DP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1114;RO=16;RPPR=3.55317 GT:DP:DPR:RO:QR:AO:QA:GL 0/0:16:16:16:1114:.:.:0 70 phiX174 1144 . C . 0 . DP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1114;RO=16;RPPR=3.55317 GT:DP:AD:RO:QR:AO:QA:GL 0/0:16:16:16:1114:.:.:0
71 phiX174 1145 . G . 0 . DP=15;DPB=15;EPPR=6.62942;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1042;RO=15;RPPR=3.15506 GT:DP:DPR:RO:QR:AO:QA:GL 0/0:15:15:15:1042:.:.:0 71 phiX174 1145 . G . 0 . DP=15;DPB=15;EPPR=6.62942;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1042;RO=15;RPPR=3.15506 GT:DP:AD:RO:QR:AO:QA:GL 0/0:15:15:15:1042:.:.:0
72 phiX174 1146 . C . 0 . DP=15;DPB=15;EPPR=6.62942;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1058;RO=15;RPPR=3.15506 GT:DP:DPR:RO:QR:AO:QA:GL 0/0:15:15:15:1058:.:.:0 72 phiX174 1146 . C . 0 . DP=15;DPB=15;EPPR=6.62942;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1058;RO=15;RPPR=3.15506 GT:DP:AD:RO:QR:AO:QA:GL 0/0:15:15:15:1058:.:.:0
73 phiX174 1147 . T . 0 . DP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=999;RO=15;RPPR=4.31318 GT:DP:DPR:RO:QR:AO:QA:GL 0/0:15:15:15:999:.:.:0 73 phiX174 1147 . T . 0 . DP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=999;RO=15;RPPR=4.31318 GT:DP:AD:RO:QR:AO:QA:GL 0/0:15:15:15:999:.:.:0
74 phiX174 1148 . C . 0 . DP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1003;RO=15;RPPR=4.31318 GT:DP:DPR:RO:QR:AO:QA:GL 0/0:15:15:15:1003:.:.:0 74 phiX174 1148 . C . 0 . DP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1003;RO=15;RPPR=4.31318 GT:DP:AD:RO:QR:AO:QA:GL 0/0:15:15:15:1003:.:.:0
75 phiX174 1149 . T C 4.04114e-07 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=37;NS=1;NUMALT=1;ODDS=16.1901;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=830;RO=13;RPL=0;RPP=5.18177;RPPR=7.18621;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=4.51363;SRR=8;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 0/0:14:14,1:13:830:1:33:0,-1.0599,-39.8344 75 phiX174 1149 . T C 4.04114e-07 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=37;NS=1;NUMALT=1;ODDS=16.1901;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=830;RO=13;RPL=0;RPP=5.18177;RPPR=7.18621;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=4.51363;SRR=8;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/0:14:13,1:13:830:1:33:0,-1.0599,-39.8344
76 phiX174 1151 . C T 3.45599e-08 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=8.59409;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=37;NS=1;NUMALT=1;ODDS=18.6491;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=946;RO=14;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=3;SRP=12.937;SRR=11;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 0/0:15:15,1:14:946:1:27:0,-1.85676,-43.833 76 phiX174 1151 . C T 3.45599e-08 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=8.59409;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=37;NS=1;NUMALT=1;ODDS=18.6491;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=946;RO=14;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=3;SRP=12.937;SRR=11;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/0:15:14,1:14:946:1:27:0,-1.85676,-43.833
77 phiX174 1152 . G . 0 . DP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=993;RO=16;RPPR=5.18177 GT:DP:DPR:RO:QR:AO:QA:GL 0/0:16:16:16:993:.:.:0 77 phiX174 1152 . G . 0 . DP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=993;RO=16;RPPR=5.18177 GT:DP:AD:RO:QR:AO:QA:GL 0/0:16:16:16:993:.:.:0
78 phiX174 1153 . T . 3.38668e-15 . DP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=880;RO=15;RPPR=4.31318 GT:DP:DPR:RO:QR:AO:QA:GL 0/0:15:15:15:880:.:.:0 78 phiX174 1153 . T . 3.38668e-15 . DP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=880;RO=15;RPPR=4.31318 GT:DP:AD:RO:QR:AO:QA:GL 0/0:15:15:15:880:.:.:0