Question: mosdepth coverage so slow - fast way to get coverage of restricted regions WES
1
gravatar for cocchi.e89
8 months ago by
cocchi.e89120
cocchi.e89120 wrote:

I am trying to check the coverage in few regions in some WES samples. I really need very few regions, this is the BED file:

2   198266460   198266618
2   198266703   198266860
2   198267274   198267556
2   198267667   198267765
2   198268303   198268494
9   5069919 5070058
9   5073692 5073791
9   5078300 5078450
17  74732949    74732969
20  31021081    31025147

I tried bedtools genomecov but it was slow, I then searched around and found few posts speaking of mosdepth that, based on their README, should take:

mosdepth --by capture.bed sample-output sample.exome.bam

For a 5.5GB exome BAM and all 1,195,764 ensembl exons as the regions, this completes in 1 minute 38 seconds with a single CPU

and mine command on a 8.6 GB WES .bam is already taking more tahn 25 minutes! Here the command:

mosdepth --by ${restrictedBed} restricted-output ${fileGenome}

and similarly with option -t 3 that should use 3 threads.

Am I not getting something? Is there a fast way to get the coverage of a limited set of regions from a BAM??

Thank you very much in advance for any help

coverage wes exome mosdepth • 368 views
ADD COMMENTlink modified 8 months ago by Biostar ♦♦ 20 • written 8 months ago by cocchi.e89120
1

Check with top if the tool is running at 100% CPU or if any bottlenecks are slowing it down.

ADD REPLYlink written 8 months ago by ATpoint44k

Are you doing the analysis on a laptop? Time comparisons are not meaningful unless there is metadata for hardware provided. Trying to compare a 15W U series laptop CPU to a 150W Xeon monster is unfair on many levels.

ADD REPLYlink written 8 months ago by GenoMax95k

Sorry, on a server machine with 48 CPUs and 128GB RAM

ADD REPLYlink written 8 months ago by cocchi.e89120

And the file is not on a slow remote disk or something? If IO or network are limiting then fast tools won't make much difference

ADD REPLYlink written 8 months ago by WouterDeCoster45k
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