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.
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