kfdrc genotype refinement workflow

Implementation of Broad Institute Genotype Refinement Workflow

Genotype Refinement workflow for germline short variants

• Note, step 4 is skipped
• variant effect predictor run at the end to annotate vcf and get variant summary stats

basic info

• tool images: https://hub.docker.com/r/kfdrc/
• dockerfiles: https://github.com/d3b-center/bixtools
• tested with
  • rabix-v1.0.5: https://github.com/rabix/bunny/releases/tag/v1.0.5

inputs:

• Uses output gvcf from https://github.com/kids-first/kf-jointgenotyping-workflow

ped:
  class: File
  path: FM_XXXXXX.ped
reference:
  class: File
  path: Homo_sapiens_assembly38.fasta
cache: File
  class: File
  path: homo_sapiens_vep_93_GRCh38_convert_cache.tar.gz # tar gzipped vep93 cache file
snp_sites:
  class: File
  path: 1000G_phase3_v4_20130502.sites.hg38.vcf
vqsr_vcf:
  class: File
  path: vqsr_vcf.vcf.gz # A recalibrated variants gvcf from VQSR
output_basename: vqsr_vcf