Mercurial > repos > greg > vsnp_get_snps

annotate test-data/input_zc_vcf.vcf @ 14:44b84d32883c draft default tip

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"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
author greg
date Mon, 15 Nov 2021 23:14:34 +0000
parents da20c7c76d06
children
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1 ##fileformat=VCFv4.2
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2 ##fileDate=20190125
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3 ##source=freeBayes v1.2.0-dirty
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4 ##reference=/scratch/analysis_staging/a_script/vcf_test_files_sra_downloaded_2019-01-23/SRR1791698/NC_002945v4.fasta
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5 ##contig=<ID=NC_002945.4,length=4349904>
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6 ##phasing=none
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7 ##commandline="freebayes -E -1 -e 1 -u --strict-vcf -f /scratch/analysis_staging/a_script/vcf_test_files_sra_downloaded_2019-01-23/SRR1791698/NC_002945v4.fasta /scratch/analysis_staging/a_script/vcf_test_files_sra_downloaded_2019-01-23/SRR1791698/SRR1791698-nodup.bam --region NC_002945.4:0-100000
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8 ##filter="QUAL > 20
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9 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR1791698
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10 NC_002945.4 1057 . A G 7624.7 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=262;CIGAR=1X;DP=265;DPB=265;DPRA=0;EPP=4.20378;EPPR=5.18177;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=60;NS=1;NUMALT=1;ODDS=363.221;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8526;QR=12;RO=1;RPL=140;RPP=5.69563;RPPR=5.18177;RPR=122;RUN=1;SAF=139;SAP=5.13204;SAR=123;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:265:1,262:1:12:262:8526:-766.088,-78.0909,0
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diff changeset
82 NC_002945.4 407246 . C G 2433.98 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=91;CIGAR=1X;DP=93;DPB=93;DPRA=0;EPP=7.04303;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=130.758;PAIRED=0.989011;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2860;QR=0;RO=0;RPL=42;RPP=4.17955;RPPR=0;RPR=49;RUN=1;SAF=14;SAP=97.7199;SAR=77;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:93:0,91:0:0:91:2860:-257.436,-27.3937,0