bedcov output meaning

Question

[amy__]

Hello,

I recently asked samtools on github this: https://github.com/samtools/samtools/issues/1662

I have whole exome sequences; I have aligned them to hg38. I want to work out the % coverage across the reference genome at the points that the bed file states were sequenced. I may be wrong but samtools coverage seems to provide these results in your example samtools coverage -r chr1:1M-12M input.bam

However, rather than just a part of the chromosome I would like to do this using the regions of the exome capture stated in the bed file.

I may be misunderstanding the use of samtools coverage, so apologies if that is the case. I have used samtools depth to work out the average depth but would like some sort of coverage across the parts of the whole exome regions to go alongside.

I was told that bedcov would be a good way to do this, so I've ran it and have an output file that looks something like this (ignore line gaps):

NC_000001.11    12080   12251   19722

NC_000001.11    12080   12251   19722

NC_000001.11    24260   24532   38887

I assume the second and third column are locations in the given capture. But I'm not sure what the final column is, does anyone have an idea?

Thanks! Amy

[Pierre Lindenbaum]

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

Reports the total read base count (i.e. the sum of per base read depths) for each genomic region specified in the supplied BED file.

[amy__]

Thanks Pierre, and does that differ from samtools depth? Which 'computes the read depth at each position or region'? Sorry lots of tools seem similar, it can get confusing. Thanks!

[Pierre Lindenbaum]

samtools depth reports the depth per base. samtools bedcovs report the sum of depth per interval.