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, 12:27, 19 August 2015
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| <div class=" mw-collapsible mw-collapsed"> | | <div class=" mw-collapsible mw-collapsed"> |
| #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 |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
− | 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] |