If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

hard-masked analysis set of GRCh38

jingmengjingmeng AustraliaMember

Hi, happy new year. It is said that in the analysis set of GRCh38, duplicate copies of centromeric and genomic repeat arrays (on chromosomes 5, 14, 19, 21, & 22) and two PAR regions on chromosome Y are hard-masked. I am not sure of the meaning of duplicate copies of repeat arrays. I know a repeat array is that some nucleotides are repeated several times, for example, ATTCGGATTCGGATTCGG (ATTCGG is repeated three times). Then what are duplicate copies for this case? Could you please provide some information (coordinate and nucleotide) of the hard-masked regions in the analysis set? And could you please explain to me why hard-masking these regions can result optimal mapping? For variant calling on the repeat and low complexity regions, as the repeat regions are hard-masked and ignored, no variant is predicted in these regions and it will result in sensitivity decreasing. Is my guess right? Look forward to hearing from you.

Issue · Github
by shlee

Issue Number
Last Updated
Closed By


Sign In or Register to comment.