hg38 low-quality site BED file

Question

[cocchi.e89]

I am working on some human WGS data hg38 assembly. I was wondering: is there any BED format to exclude low-quality sites?

Thank you very much in advance!

[GenoMax]

Are you referring to the mappability files?

[igor]

See also: Where to download blacklisted regions?

Answer 1

[Pierre Lindenbaum]

the complement of wgs_calling_regions.hg38.interval_list under https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0/ ?

[cocchi.e89]

What are these regions exactly?

[GenoMax]

See last para on this page: https://gatk.broadinstitute.org/hc/en-us/articles/360035531852-Intervals-and-interval-lists

[cocchi.e89]

Thus, these are the intervals to include (not intervals to exclude). Right? Did I understand correctly?

[GenoMax]

That is why @Pierre said

the complement of wgs_calling_regions.hg38.interval_list

[cocchi.e89]

Thank so much GenoMax