genomics-variant-calling

To perform germline variant calling, you use GATK HaplotypeCaller or DeepVariant to analyze SAM/BAM alignment files, generating a VCF output that lists all identified single nucleotide polymorphisms and insertions/deletions present in the sample.

Germline variant calling identifies inherited genetic variations using GATK HaplotypeCaller or DeepVariant, while somatic variant calling detects acquired tumor mutations using GATK Mutect2, both producing VCF outputs from SAM/BAM alignment files.

Variant quality control applies VQSR or hard filtering to the initial VCF output to distinguish true biological genetic signals from technical sequencing noise, ensuring high-quality SNV and Indel variant calls for downstream analysis.

Yes, the variant calling workflow includes a specific GVCF workflow utilizing GATK HaplotypeCaller to record both called and uncalled genomic sites, enabling accurate joint genotyping across multiple sequencing samples.

Yes, you can use GATK Mutect2 or FreeBayes for somatic variant calling. These tools analyze SAM/BAM alignment files to detect acquired somatic SNVs and Indels, generating a VCF output for downstream genomic analysis.

The best way to call variants from whole-genome sequencing data is using GATK HaplotypeCaller or DeepVariant to analyze BAM files, followed by VQSR or hard filtering for quality control to produce high-confidence VCF outputs.