08. Troubleshooting - cbg-ethz/LongSom GitHub Wiki

Computational Bottlenecks

Somatic variants detection

The main computational bottleneck (time-wise) in workflow/rules/SNVCalling.smk is the rule BaseCellCounter. If you cannot use more threads (or do not have access to an HPC), please consider splitting the input BAM file per chromosome, and run LongSom on each chromosome.