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. --dna-variants-tsv-file takes either a call-somatic-dna-vars table or a TSV in the variant grammar with the columns origin, variant_id, chromosome_1, position_1, strand_1, operation_1, chromosome_2, position_2, strand_2, operation_2 and sequence. Columns are matched by name. VSTOL converts the outputs of other variant callers to this grammar.

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.