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| === Discover2 === | | === Discover2 === |
| | | |
− | Discovers variants from reads in a BAM or CRAM file. | + | Discovers variants from reads in a BAM/CRAM file. |
| | | |
| <div class=" mw-collapsible mw-collapsed"> | | <div class=" mw-collapsible mw-collapsed"> |
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| vt discover -b NA12878.bam -s NA12878 -r hs37d5.fa -i 20 -v snps,indels,mnps | | vt discover -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 discover [options]
| + | usage : vt discover2 [options] |
| | | |
− | options : -b input BAM file
| + | options : -b input BAM/CRAM file |
− | -v variant types [snps,mnps,indels]
| + | -y soft clipped unique sequences cutoff [0] |
− | -f fractional evidence cutoff for candidate allele [0.1]
| + | -x soft clipped mean quality cutoff [0] |
− | -e evidence count cutoff for candidate allele [2]
| + | -w insertion desired type II error [0.0] |
− | -q base quality cutoff for bases [13]
| + | -c insertion desired type I error [0.0] |
− | -m MAPQ cutoff for alignments [20]
| + | -h insertion fractional evidence cutoff [0] |
− | -s sample ID
| + | -g insertion count cutoff [1] |
− | -r reference sequence fasta file []
| + | -n deletion desired type II error [0.0] |
− | -o output VCF file [-]
| + | -m deletion desired type I error [0.0] |
− | -I file containing list of intervals []
| + | -v deletion fractional evidence cutoff [0] |
− | -i intervals []
| + | -u deletion count cutoff [1] |
− | -- ignores the rest of the labeled arguments following this flag
| + | -k snp desired type II error [0.0] |
− | -h displays help
| + | -j snp desired type I error [0.0] |
| + | -f snp fractional evidence cutoff [0] |
| + | -e snp evidence count cutoff [1] |
| + | -q base quality cutoff for bases [0] |
| + | -C likelihood ratio cutoff [0] |
| + | -B reference bias [0] |
| + | -a read exclude flag [0x0704] |
| + | -l ignore overlapping reads [false] |
| + | -t MAPQ cutoff for alignments [0] |
| + | -p ploidy [2] |
| + | -s sample ID |
| + | -r reference sequence fasta file [] |
| + | -o output VCF file [-] |
| + | -z ignore MD tags [0] |
| + | -d debug [0] |
| + | -I file containing list of intervals [] |
| + | -i intervals [] |
| + | -? displays help |
| | | |
| </div> | | </div> |