Question

hg38 low-quality site BED file

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2.1 years ago

cocchi.e89 ▴ 280

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!

human low-quality-site BED hg38 • 1.9k views

ADD COMMENT • link 2.1 years ago by cocchi.e89 ▴ 280

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Are you referring to the mappability files?

ADD REPLY • link 2.1 years ago by GenoMax 147k

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ADD REPLY • link 2.1 years ago by igor 13k

score 2 · Accepted Answer · 2022-10-26

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2.1 years ago

Pierre Lindenbaum 164k

ADD COMMENT • link 2.1 years ago by Pierre Lindenbaum 164k

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What are these regions exactly?

ADD REPLY • link 2.1 years ago by cocchi.e89 ▴ 280

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ADD REPLY • link 2.1 years ago by GenoMax 147k

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

ADD REPLY • link 2.1 years ago by cocchi.e89 ▴ 280

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That is why @Pierre said

the complement of wgs_calling_regions.hg38.interval_list

ADD REPLY • link 2.1 years ago by GenoMax 147k

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Thank so much GenoMax

ADD REPLY • link 2.1 years ago by cocchi.e89 ▴ 280