I used genome music to calculate significant pathways, which works great.
In the first, where coverage is calculated,
genome music bmr calc-covg --gene-covg-dir geneCov_combined --bam-list $bamList --output-dir $outDir --reference-sequence $assembly --roi-file $roi
This step is very time consuming when you have 100s of samples.
Is there any way if this can be run in parallel ?
I think, dividing sample into subgroups also does not work here.
Any suggestions ?