Read depths on whole genome (WGS)

Hello to the whole community

I have aligned a WGS data and I want to read the coverage of a region of interest (chr9:27,573,456-27,573,614). I know that samtools depth can read the coverage base by base, but I don't know how to delimit a portion of my bam. Can anyone help me please?

Thanks to all

samtools wgs read-depth

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updated 3.1 years ago by Ram

• written 4.3 years ago by Jean-Charles •

1 answer

http://www.htslib.org/doc/samtools-depth.html

-r CHR:FROM-TO Only report depth in specified region.

samtools depth -r "chr1:234-567" in.bam

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written 4.3 years ago by Pierre Lindenbaum

Thank you so much

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written 4.3 years ago by Jean-Charles •

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