DNA Variant Calling

Use this skill as the DNA variant-calling dispatcher for WGS, WES, or targeted DNA panel analysis from FASTQ, BAM, or CRAM. Once the sample model is clear, hand off to the narrow subtype skill.

Essential Inputs

Confirm:

• data type: WGS, WES, or panel
• sample model: germline single sample, cohort, trio, tumor-only, or tumor-normal
• input type: FASTQ, BAM, or CRAM
• organism and reference genome
• known-sites resources for BQSR, if required
• target BED for WES or panels
• UMI or duplex handling
• desired callers and annotation outputs

Dispatch