Mercurial > repos > iuc > lofreq_call

annotate test-data/call-out1.vcf @ 5:65432c3abf6c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 841c48994eb214a2f8718b1d1aca22bc38598528"
author iuc
date Mon, 15 Jun 2020 13:13:03 -0400
parents 074d44697036
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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1 ##fileformat=VCFv4.0
5
65432c3abf6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 841c48994eb214a2f8718b1d1aca22bc38598528"
iuc
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2 ##fileDate=20200615
65432c3abf6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 841c48994eb214a2f8718b1d1aca22bc38598528"
iuc
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3 ##source=lofreq call --verbose --ref reference.fa --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/tmpe0171355/job_working_directory/000/28/working/pp-tmp/lofreq2_call_parallell2yprl2k/0.vcf.gz reads.bam
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31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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4 ##reference=reference.fa
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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5 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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6 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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7 ##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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8 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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9 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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10 ##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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11 ##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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12 ##FILTER=<ID=min_snvqual_38,Description="Minimum SNV Quality (Phred) 38">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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13 ##FILTER=<ID=min_indelqual_20,Description="Minimum Indel Quality (Phred) 20">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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14 ##FILTER=<ID=min_dp_10,Description="Minimum Coverage 10">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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15 ##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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16 ##FILTER=<ID=min_snvqual_38,Description="Minimum SNV Quality (Phred) 38">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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17 ##FILTER=<ID=min_indelqual_20,Description="Minimum Indel Quality (Phred) 20">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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18 #CHROM POS ID REF ALT QUAL FILTER INFO
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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19 pBR322 1134 . C T 49314 PASS DP=1767;AF=1.000000;SB=0;DP4=0,0,910,857