LUMC/hutspot: Version 1.2.0

Hutspot

This is a multisample DNA variant calling pipeline for use in diagnostics based on Snakemake, bwa and the GATK HaplotypeCaller.

Features

• Any number of samples is supported
• Whole-genome calling, regardless of wet-lab library preparation.
• Follows modern best practices
  • Each sample is individually called as as a GVCF.
  • A multisample VCF is then produced by genotyping the collection of GVCFs.
• Data parallelization for calling and genotyping steps.
  • Using ~100 chunks, we call an entire exome in ~15 minutes!
• Reasonably fast.
  • 96 exomes in < 24 hours.
• No unnecessary jobs
• Coverage metrics for any number of bed files.
• Fully containerized rules through singularity and biocontainers. Legacy conda environments are available as well.
• Optionally sub-sample inputs when number of bases exceeds a user-defined threshold