Service notice: Several of our team members are on vacation so service will be slow through at least July 13th, possibly longer depending on how much backlog accumulates during that time. This means that for a while it may take us more time than usual to answer your questions. Thank you for your patience.

hard-masked analysis set of GRCh38

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.