- Fix RevertSam to SANITIZE output when read group information is missing (#856). The tool considers read group (
RG) information missing if the SAM file header does not have an
@RGline, the read does not have an
RGtag or the tag’s read group is absent from header groups.
- For deprecated CrosscheckReadGroupFingerprints, fix option
- Fingerprinting tools now read a HaplotypeMap object from a VCF (#793). Previously, tools could only read a custom-formatted file. The VCF needs to have exactly one sample, HET for all the variants, and haplotype block phasing via phased genotypes (0|1, and 1|0) and the
PSformat field. The
AFfield is the AlternateAllele frequency, NOT the minor allele frequency, as it is in the HaplotypeDatabase file. For more details on the file formats, see GATK Article#9526.