Differences in WES Coverage Values (Mosdepth Versions 0.3.3 and 0.3.8)

[niyati1211]

I ran mosdepth twice on the same WES samples and got different coverage values. I used the same exome intervals bed file and reference genome build (hg38). There version of mosdepth used was different between both runs: 0.3.3 vs 0.3.8. Mosdepth was run within the nf-core/Sarek pipeline.

For example, in one of the samples, the median coverage is 69x (0.3.3) vs 100x (0.3.8). I am confused as to why there is such a large difference. Is this expected? Any insight will be appreciated!

[brentp]

hi, I suspect the difference is in how your pipeline is calling mosdepth. Can you show the actual arguments sent to mosdepth for each run?

[niyati1211]

Thank you for the quick response, brent!

So I believe this is how the pipeline calls mosdepth (https://github.com/nf-core/sarek/blob/f034b737630972e90aeae851e236f9d4292b9a4f/conf/modules/modules.config#L54). I am not sure if the arguments sent to mosdepth were different between both runs since I was using different versions of the pipeline (the older version of the pipeline using 0.3.3 and new version uses 0.3.8). I will have to check with the nf-core/sarek support team.

withName: 'MOSDEPTH' {
       ext.args = { !params.wes ? "-n --fast-mode --by 500" : ""}
       ext.prefix       = {
           if (params.tools && params.tools.split(',').contains('sentieon_dedup')) {
               "${meta.id}.dedup"
           } else if (params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) {
               "${meta.id}.sorted"
           } else {
               "${meta.id}.md"
           }
       }
       ext.when         = { !(params.skip_tools && params.skip_tools.split(',').contains('mosdepth')) }
       publishDir = [
           mode: params.publish_dir_mode,
           path: { "${params.outdir}/reports/mosdepth/${meta.id}" },
           saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
       ]
   }

   if ((params.step == 'mapping' || params.step == 'markduplicates'|| params.step == 'prepare_recalibration'|| params.step == 'recalibrate') && (!(params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator')))) {
       withName: 'NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH' {
           ext.prefix       = { "${meta.id}.recal" }
       }

       withName: 'NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS' {
           ext.prefix       = { "${meta.id}.recal.cram" }
           ext.when         = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) }
           publishDir       = [
               mode: params.publish_dir_mode,
               path: { "${params.outdir}/reports/samtools/${meta.id}" },
               saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
           ]
       }
   }