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telatin / bamtocov

🏔 coverage extraction from BAM/CRAM files, supporting targets 📊  
https://telatin.github.io/bamtocov/
MIT License
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[BUG] run time exceeds > 6 hours human exome #12

Open ESDeutekom opened 2 months ago

ESDeutekom commented 2 months ago

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):

HuiyangYu commented 1 month ago

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.