Forum Login Issue:
Currently the "Log in with Google" button redirects you to a "Page not found." Our forum vendors have implemented a fix, and now we are just waiting on a patch to be released. In the meantime, while on the "Page not found" you can edit the URL to delete the second gatk, firecloud, or wdl (depending on what subforum you are acessing).
ex: https://gatkforums.broadinstitute.org/gatk/gatk/entry/...

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
1619
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
sooheelee

Answers

Sign In or Register to comment.