[BUG] run time exceeds > 6 hours human exome

[ESDeutekom]

Describe the bug
Dear bamtocov team,

I have human WES data and am trying to run bamtocov. After 6 hours, not even half is done/calculated, even when using 24 threads. Maybe I am missing something?

To Reproduce
bamtocov EF_V1_S9.MD.sorted.bam --regions Targets_hg38.bed --threads 24 --mapq 20 > EF_V1.cov

Expected behavior
From the paper I gather it should run a lot faster than 6 hours.

System information (please complete the following information):

• OS: Linux
• Browser [e.g. chrome, safari]
• Version: 2.7.0

[HuiyangYu]

BamToCov is suitable for statistical analysis of whole-genome sequencing data, but not suitable for exome sequencing data. You might want to try PanDepth instead, as it provides very fast statistical analysis specifically designed for exome sequencing data.

[telatin]

Hi @ESDeutekom ,
bamtocov is a generic tool for coverage calculation. It excels in having the lower memory footprint but in your case I would try MosDepth for complete reports and probably lower times.

I never had runtime so long as 6 hours for a human exome, so it could be the target is the gricky part in this case. Could you please share your Bed?