Tagged with #pseudoautosomalregion
0 documentation articles | 0 announcements | 1 forum discussion

No posts found with the requested search criteria.
No posts found with the requested search criteria.

Created 2012-12-11 09:55:31 | Updated | Tags: unifiedgenotyper pseudoautosomalregion
Comments (6)

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