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usage : vt discover [options]
usage : vt discover [options]
options : -b input BAM file
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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