Somatic DNA Variants

Use this skill for tumor-normal or tumor-only somatic SNV/indel calling from FASTQ, BAM, or CRAM. If the request is inherited germline calling or family analysis, use ngs-dna-germline-variants.

Essential Inputs

Confirm:

• tumor-normal, tumor-only, relapse-baseline, or multi-tumor design
• WGS, WES, or panel assay and target BED when applicable
• input type and whether reads are already aligned
• tumor/normal pairing table and sample identifiers
• reference build, known-sites, germline resource, and annotation cache
• panel-of-normals availability and matched-normal availability
• tumor purity, contamination expectations, and minimum allele fraction goals
• desired outputs: raw calls, filtered calls, VEP/SnpEff annotation, MAF, CNV/SV handoff

Route