FAQ

Frequently asked questions. If your question isn’t answered here, please open an issue.

Inputs

NoteFor integrate-vars can I supply a DNA variant callset from another method?

Yes, but the variant callset format must be in the Occam’s Grammar format (TSV). You can do this using VSTOL.

NoteHow do I avoid out-of-memory errors on large BAMs?

Exacto’s DNA variant callers (call-germline-dna-vars and call-somatic-dna-vars) hold per-read evidence in memory while clustering variant candidates. If your Exacto job runs out of memory, you can:

• Reduce --num-threads to lower concurrent peak memory.
• Reduce --chunk-size (default: 100,000) for call-germline-dna-vars / call-somatic-dna-vars.