How to turn off joint genotyping in multisample calling

[tnguyengel]

What parameters should we use if we want the genotypes in the single-sample call to match the genotypes from the multi-sample calls?

EG)

• single sample: site=HOM_REF with strong support --> multisample: site = HOM_REF for that sample
• single sample: site = HET/HOM_ALT with strong support --> multisample: site = HET/HOM_ALT for that sample
• single sample: site = variant might exist but fails QC --> multisample: site = missing for that sample

Would these parameters be sufficient?

Sniffles per-sample calling:

sniffles \
        -i [in_bam] \
        -v [out_vcf] \
        --snf [out_snf] \
        --sample-id [sample_id] \
        --output-rnames \
        --qc-output-all

Sniffles multisample calling:

sniffles \
        --input [snf_sample_id_tsv] \
        --vcf [out_merged_vcf] \
        --combine-high-confidence 0 \
        --combine-low-confidence 1.1 \
        --combine-low-confidence-abs [total samples + 1]  \
        --combine-null-min-coverage 1