Github.com/gatk-workflows/gatk4-basic-variant-validation/gatk4-basic-variant-validation

gatk4-basic-variant-validation

Simple workflow to validate a VCF (or GVCF) – NOT Best Practices, only for teaching/demo purposes.

Inputs and outputs

Required inputs

  • One VCF file or GVCF file and its index (can be bgzip/tabix)
  • A list of intervals to process (for parallelization)
  • Genomic resources: reference genome in FASTA format (.fasta) and its accessory files (.fasta.fai and .dict)

Optional inputs

  • Resourcing and environment parameters including memory, disk space a

This is a companion discussion topic for the original entry at github.com/gatk-workflows/gatk4-basic-variant-validation/gatk4-basic-variant-validation