gatk-variant-calling

To call SNPs and indels from WGS BAM files, this Skill automates the GATK Best Practices pipeline by orchestrating HaplotypeCaller, GenomicsDBImport, GenotypeGVCFs, and variant filtration. It integrates with samtools and bcftools for necessary pre- and post-processing tasks.

For joint genotyping across multiple samples, the pipeline uses GATK's GenomicsDBImport and GenotypeGVCFs to consolidate GVCF files. This enables comprehensive population studies and accurate variant detection across your entire cohort of WGS or WES data.

Yes, the GATK pipeline includes Base Quality Score Recalibration (BQSR) as a core feature to enhance variant calling accuracy. This data quality improvement step adjusts base quality scores in your BAM files before the actual variant calling process begins.

Yes, you need pre-processed BAM files and reference genome files to execute the germline variant calling pipeline. The Skill requires these inputs to successfully run HaplotypeCaller and subsequent GATK Best Practices steps.