Germline DNA Variants

Use this skill for germline WGS, WES, or inherited-disease panel analysis from FASTQ, BAM, or CRAM. If the request is tumor-only, tumor-normal, or low-frequency molecular-barcode panel calling, use a somatic or UMI-panel skill instead.

Essential Inputs

Confirm:

• data type: WGS, WES, or targeted panel
• sample model: singleton, cohort, duo, trio, family, or case/control
• input type: FASTQ, BAM, or CRAM
• organism, reference build, FASTA, indexes, and contig naming
• known-sites resources for BQSR, contamination, and annotation
• target BED and bait BED for WES/panel data
• sex/ploidy assumptions and mitochondrial/sex-chromosome requirements
• desired callers, annotation outputs, and final VCF/gVCF expectations

Route