Mercurial > repos > iuc > vcfanno

comparison test-data/vcfanno_result.vcf @ 1:cdcaa40e5e45 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/vcfanno/ commit c08085bc808613dd2b1a34d53e8366fafbda5ec7"
author iuc
date Mon, 06 Dec 2021 09:23:38 +0000
parents fb20fa735dfe
children
comparison
equal deleted inserted replaced
0:fb20fa735dfe 1:cdcaa40e5e45
145 ##phasing=none 145 ##phasing=none
146 ##commandline="/mnt/thor_pool1/user_data/cc2qe/code/speedseq/bin/freebayes -f /shared/genomes/b37/full/human_g1k_v37.fasta --region MT:12136..12498 bam/NA12877_S1/NA12877_S1.bam bam/NA12878_S1/NA12878_S1.bam bam/NA12879_S1/NA12879_S1.bam bam/NA12880_S1/NA12880_S1.bam bam/NA12881_S1/NA12881_S1.bam bam/NA12882_S1/NA12882_S1.bam bam/NA12883_S1/NA12883_S1.bam bam/NA12884_S1/NA12884_S1.bam bam/NA12885_S1/NA12885_S1.bam bam/NA12886_S1/NA12886_S1.bam bam/NA12887_S1/NA12887_S1.bam bam/NA12888_S1/NA12888_S1.bam bam/NA12889_S1/NA12889_S1.bam bam/NA12890_S1/NA12890_S1.bam bam/NA12891_S1/NA12891_S1.bam bam/NA12892_S1/NA12892_S1.bam bam/NA12893_S1/NA12893_S1.bam" 146 ##commandline="/mnt/thor_pool1/user_data/cc2qe/code/speedseq/bin/freebayes -f /shared/genomes/b37/full/human_g1k_v37.fasta --region MT:12136..12498 bam/NA12877_S1/NA12877_S1.bam bam/NA12878_S1/NA12878_S1.bam bam/NA12879_S1/NA12879_S1.bam bam/NA12880_S1/NA12880_S1.bam bam/NA12881_S1/NA12881_S1.bam bam/NA12882_S1/NA12882_S1.bam bam/NA12883_S1/NA12883_S1.bam bam/NA12884_S1/NA12884_S1.bam bam/NA12885_S1/NA12885_S1.bam bam/NA12886_S1/NA12886_S1.bam bam/NA12887_S1/NA12887_S1.bam bam/NA12888_S1/NA12888_S1.bam bam/NA12889_S1/NA12889_S1.bam bam/NA12890_S1/NA12890_S1.bam bam/NA12891_S1/NA12891_S1.bam bam/NA12892_S1/NA12892_S1.bam bam/NA12893_S1/NA12893_S1.bam"
147 ##VEP=v76 cache=/shared/external_bin/ensembl-tools-release-76/cache/homo_sapiens/76_GRCh37 db=. 147 ##VEP=v76 cache=/shared/external_bin/ensembl-tools-release-76/cache/homo_sapiens/76_GRCh37 db=.
148 ##SnpEffVersion="3.6c (build 2014-05-20), by Pablo Cingolani" 148 ##SnpEffVersion="3.6c (build 2014-05-20), by Pablo Cingolani"
149 ##SnpEffCmd="SnpEff GRCh37.75 " 149 ##SnpEffCmd="SnpEff GRCh37.75 "
150 ##vcfanno=0.3.3
150 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12889 NA12890 NA12877 151 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12889 NA12890 NA12877
151 1 10492 . C T 3055.1 . AB=0.188084;ABP=726.385;AC=9;AF=0.264706;AN=34;AO=167;CIGAR=1X;TYPE=snp;mapq=55.5;coverage=12;xdp2=4,8 GT:DP:RO:QR:AO:QA:GL 0/0:117:117:3837:0:0:0,-10,-10 0/0:113:113:3758:0:0:0,-10,-10 0/0:132:132:4396:0:0:0,-10,-10 152 1 10492 . C T 3055.1 . AB=0.188084;ABP=726.385;AC=9;AF=0.264706;AN=34;AO=167;CIGAR=1X;TYPE=snp;mapq=55.5;coverage=12;xdp2=4,8 GT:DP:RO:QR:AO:QA:GL 0/0:117:117:3837:0:0:0,-10,-10 0/0:113:113:3758:0:0:0,-10,-10 0/0:132:132:4396:0:0:0,-10,-10
152 1 10583 . G A 1071.5 . AB=0.191964;ABP=372.238;AC=8;AF=0.235294;AN=34;AO=104;CIGAR=1X;TYPE=snp;mapq=52.6667;coverage=3;xdp2=1,2 GT:DP:RO:QR:AO:QA:GL 0/1:61:40:1252:20:580:-10,0,-10 0/0:57:51:1697:6:175:-6.44272,0,-10 0/0:64:56:1738:7:207:-8.6143,0,-10 153 1 10583 . G A 1071.5 . AB=0.191964;ABP=372.238;AC=8;AF=0.235294;AN=34;AO=104;CIGAR=1X;TYPE=snp;mapq=52.6667;coverage=3;xdp2=1,2 GT:DP:RO:QR:AO:QA:GL 0/1:61:40:1252:20:580:-10,0,-10 0/0:57:51:1697:6:175:-6.44272,0,-10 0/0:64:56:1738:7:207:-8.6143,0,-10
153 1 10616 . CCGCCGTTGCAAAGGCGCGCCG C 580.2 . AB=0.4375;ABP=3.55317;AC=31;AF=0.911765;AN=34;AO=54;CIGAR=1M21D1M;TYPE=del;mapq=21;coverage=1;xdp2=0,1 GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:35:-3.325,-0.60206,0 1/1:5:0:0:4:106:-9.744,-1.20412,0 1/1:9:0:0:9:208:-10,-2.70927,0 154 1 10616 . CCGCCGTTGCAAAGGCGCGCCG C 580.2 . AB=0.4375;ABP=3.55317;AC=31;AF=0.911765;AN=34;AO=54;CIGAR=1M21D1M;TYPE=del;mapq=21;coverage=1;xdp2=0,1 GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:35:-3.325,-0.60206,0 1/1:5:0:0:4:106:-9.744,-1.20412,0 1/1:9:0:0:9:208:-10,-2.70927,0
154 1 10623 . TGCAAAGGC CGCAAAG 580.2 . AB=0.375;ABP=5.18177;AC=3;AF=0.0882353;AN=34;AO=10;CIGAR=7M1X6M2D7M;TYPE=complex GT:DP:RO:QR:AO:QA:GL ./.:2:0:0:0:0:-3.325,-3.325,-3.325 ./.:5:0:0:0:0:-9.744,-9.744,-9.744 ./.:9:0:0:0:0:-10,-10,-10 155 1 10623 . TGCAAAGGC CGCAAAG 580.2 . AB=0.375;ABP=5.18177;AC=3;AF=0.0882353;AN=34;AO=10;CIGAR=7M1X6M2D7M;TYPE=complex GT:DP:RO:QR:AO:QA:GL ./.:2:0:0:0:0:-3.325,-3.325,-3.325 ./.:5:0:0:0:0:-9.744,-9.744,-9.744 ./.:9:0:0:0:0:-10,-10,-10