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| | = Variant Calling = | | = Variant Calling = |
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| − | === Discover ===
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| − | Discovers variants from reads in a BAM file.
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| − | <div class=" mw-collapsible mw-collapsed">
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| − | #discover variants from NA12878.bam and write to stdout
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| − | vt discover -b NA12878.bam -s NA12878 -r hs37d5.fa -i 20 -v snps,indels,mnps
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| − | <div class="mw-collapsible-content">
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| − | usage : vt discover [options]
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| − | options : -b input BAM file
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| − | -v variant types [snps,mnps,indels]
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| − | -f fractional evidence cutoff for candidate allele [0.1]
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| − | -e evidence count cutoff for candidate allele [2]
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| − | -q base quality cutoff for bases [13]
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| − | -m MAPQ cutoff for alignments [20]
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| − | -s sample ID
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| − | -r reference sequence fasta file []
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| − | -o output VCF file [-]
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| − | -I file containing list of intervals []
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| − | -i intervals []
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| − | -- ignores the rest of the labeled arguments following this flag
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| − | -h displays help
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| − | </div>
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| − | </div>
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| | === Discover2 === | | === Discover2 === |
