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#discover variants from NA12878.bam and write to stdout
#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
vt discover2 -b NA12878.bam -s NA12878 -r hs37d5.fa -i 20 -v snps,indels,mnps
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usage : vt discover2 [options]
usage : vt discover2 [options]
options : -b input BAM/CRAM file
options : -b input BAM/CRAM file
-y soft clipped unique sequences cutoff [0]
-y soft clipped unique sequences cutoff [0]
-x soft clipped mean quality cutoff [0]
-x soft clipped mean quality cutoff [0]
