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