7aba5a2f9f
-- Bugfix for BAMs containing reads without real (M,I,D,N) operators. Simply needed to set validation stringency to SILENT in the read. Added a BadCigar filter to the SAMRecord stream anyway -- Add capture all sites mode to AssessNA12878: will write all sites to the badSites VCF, regardless of whether they are bad. It's useful if you essentially want to annotate a VCF with KB information for later analysis, such as computing ROC curves -- Add ignore filters mode to AssessNA12878: will as expected treat all sites in the input VCF calls as PASS, even if the site has a FILTER field setting -- Add minPNonRef argument to AssessNA12878: this will consider a site not called even if the NA12878 genotype is not 0/0 if the PLs are present and the PL for 0/0 isn't greater than this value. It allows us to easily differentiate low confidence non-ref sites obtained via multi-sample calling from highly confident non-ref calls that might be real TP or FPs |
||
|---|---|---|
| licensing | ||
| protected | ||
| public | ||
| settings | ||
| .gitignore | ||
| README.md | ||
| build.xml | ||
| intellij_example.tar.bz2 | ||
| ivy.xml | ||