I ran Sarek on sequencing coming from two different library preps for the same sample. I am having trouble understanding/interpreting the Mosdepth Average coverage per contig graph - feel free to point me somewhere else but I am not sure if maybe I did the wrong genome. I used

nextflow run nf-core/sarek -r 3.4.2 -profile singularity --input ${sampleSheet} --outdir ${outDir} --tools mutect2,strelka,vep --genome GATK.GRCh38

But in the multiQC mosdepth graph I don't see the regular chromosomes??

My guess is that the problem here is too many contigs to fit on the x-axis. The

GATK.GRCh38

assembly contains thousands of contigs (not dozens), most of them decoys. You can see on the left

chr1

, I think that is a "representative" for all the canonical chromosomes (plus likely more contigs). If you could "zoom in", you would see all the separate ones. I am not sure how Mosdepth interacts with the intervals file, but that should actually remove most/all of the noncanonical chromosomes (there is a "default" one from GATK, designed for WGS, which removes centromers/telomers. etc., and if you have WES [use

--wes

] you need to specify your [padded] targets file) ...

Thank you, this is great!!!