Version Compatibility

Reference examples tested with: BWA-MEM2 2.2.1+, Ensembl VEP 111+, GATK 4.5+, bcftools 1.19+, fastp 0.23+, samtools 1.19+

Before using code patterns, verify installed versions match. If versions differ:

• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

FASTQ to Variants Workflow

"Call variants from my whole-genome or exome FASTQ files" → Orchestrate fastp QC, BWA-MEM2 alignment, duplicate marking, BQSR, GATK HaplotypeCaller variant calling, and VQSR/hard filtering to produce filtered VCF output.

Complete pipeline from raw DNA sequencing FASTQ files to filtered variant calls.

Workflow Overview