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mquinodo / OFF-PEAK

CNV detection tool for WES data
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Unclear what the coverage value returned by 02_coverage-count.sh means #4

Closed radinagg closed 2 months ago

radinagg commented 3 months ago

Hi there,

I am trying to quantify the percentage of on- and off-target reads in a bunch of BAM files from a targeted sequencing experiment performed using a small custom panel. To do this, I ran the first two steps of OFF-PEAK, but I am having some trouble interpreting the coverage value returned by 02_coverage-count.sh. Can you explain if this corresponds to the number of bases within a given region that are covered by at least one read or, alternatively, the number of reads that map to that region (seems most likely based on the values)?

This is how I obtained the values: bash 02_coverage-count.sh --listBAM bam_files_list.txt --mosdepth mosdepth --work outputs --targetsBED data/twist-custom-panel.bed

Thanks in advance, Radina

mquinodo commented 2 months ago

Dear Radina,

Thank you for using OFF-PEAK. OFF-PEAK is using mosdepth which is outputting the sum of per base coverage. So if your region has only one read of 150bp, the coverage will be 150. If you want the number of reads, then you need to divid by your read length. I hope that answers your question.

Best regards, Mathieu

radinagg commented 2 months ago

That's clear, thanks for the info!