From Genome Analysis Wiki
Jump to navigationJump to search
948 bytes removed
, 15:52, 25 November 2015
Line 1,088: |
Line 1,088: |
| = Variant Calling = | | = Variant Calling = |
| | | |
− |
| |
− | === Discover ===
| |
− |
| |
− |
| |
− | Discovers variants from reads in a BAM file.
| |
− |
| |
− | <div class=" mw-collapsible mw-collapsed">
| |
− | #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
| |
− | <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>
| |
| | | |
| === Discover2 === | | === Discover2 === |