1,102
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Discover
#merge duplicate variants and save output in mills.merged.vcf
#merge duplicate variants and save output in mills.merged.vcf
vt mergedups mills.vcf -o mills.merged.vcf
vt mergedups mills.vcf -o mills.merged.vcf
vt discover -b NA12878.bam -s NA12878 -r ~/ref/genome/hs37d5.fa -i 20 -v snps,indels,mnps
<div class="mw-collapsible-content">
<div class="mw-collapsible-content">
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
</div>
</div>
</div>
</div>
