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?
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.
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):