variant-calling

You can automate a GATK4 germline pipeline by orchestrating BWA-MEM2 alignment, BQSR, and HaplotypeCaller using standardized best-practice decision logic to process raw FASTQ files into variant calls.

Filtering VCF files based on ACMG criteria involves applying clinical filtering scripts that evaluate population frequency and pathogenicity scores to generate a prioritized TSV of candidate variants for clinical review.

Yes, the somatic short variant calling pipeline supports Mutect2 for variant detection and utilizes VEP for production-grade variant annotation, running end-to-end alongside standard bioinformatics toolsets like samtools and bcftools.

Cohort-based joint genotyping and VQSR filtering are fully supported to aggregate individual sample variant calls and apply variant quality score recalibration for high-confidence genomic analysis.

Yes, you need BWA-MEM2 for alignment and samtools for BAM file manipulation, alongside bcftools, pysam, VEP, and GATK4, to execute the end-to-end germline and somatic short-variant calling pipelines.

Variant calling fails due to reference inconsistency and parameter selection errors when pipelines lack standardized decision logic, which this approach prevents by enforcing best-practice parameters and reference consistency for GATK4.