Bug Bulletin: The recent 3.2 release fixes many issues. If you run into a problem, please try the latest version before posting a bug report, as your problem may already have been solved.

Does the UG call variants in pseudoautosomal regions correctly?

evakoeevakoe Posts: 24Member

Dear GATK team,

when I use the UnifiedGenotyper to call variants in chrX and/or chrY with ploidy=2, does the program call the variants and genotypes in the pseudoautosomal regions PAR1 and PAR2 correctly? More specifically, does the UG acknowledge that these regions are homologous on the X and Y chromosome, even though they differ in chromosomal position? If the UG does not take care of this by default, is there a way I can handle this? I read point 6 of this page, but I could not find the answer there:
http://www.broadinstitute.org/gatk/guide/article?id=1237

Thanks alot
Eva

Best Answer

Answers

Sign In or Register to comment.