Mercurial > repos > dave > lofreq_call

annotate test-data/call-out1.vcf @ 0:b37a6b94e9fe draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
author dave
date Wed, 27 Nov 2019 15:25:33 +0000
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b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
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1 ##fileformat=VCFv4.0
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
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2 ##fileDate=20191125
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
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3 ##source=lofreq call --ref reference.fa --no-default-filter -r pBR322:1-2180 -o /tmp/lofreq2_call_parallel3mrmthi_/0.vcf.gz alignments.bam
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
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4 ##reference=reference.fa
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
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5 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
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6 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
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7 ##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
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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">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
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9 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
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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).">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
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11 ##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
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12 ##FILTER=<ID=min_snvqual_38,Description="Minimum SNV Quality (Phred) 38">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
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13 ##FILTER=<ID=min_indelqual_20,Description="Minimum Indel Quality (Phred) 20">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
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14 ##FILTER=<ID=min_dp_10,Description="Minimum Coverage 10">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
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15 ##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
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16 ##FILTER=<ID=min_snvqual_38,Description="Minimum SNV Quality (Phred) 38">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
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17 ##FILTER=<ID=min_indelqual_20,Description="Minimum Indel Quality (Phred) 20">
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
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18 #CHROM POS ID REF ALT QUAL FILTER INFO
b37a6b94e9fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
dave
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19 pBR322 1134 . C T 49314 PASS DP=1767;AF=1.000000;SB=0;DP4=0,0,910,857