🔬 Alignment workflow for Kids-First DRC
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readme.md

kfdrc alignment workflow

basic info

references:

inputs:

  input_bam: input.bam
  indexed_reference_fasta: Homo_sapiens_assembly38.fasta
  reference_dict: Homo_sapiens_assembly38.dict
  sequence_grouping_tsv: sequence_grouping.txt
  knownsites:
  - 1000G_omni2.5.hg38.vcf.gz
  - 1000G_phase1.snps.high_confidence.hg38.vcf.gz
  - Homo_sapiens_assembly38.known_indels.vcf.gz
  - Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
  dbsnp_vcf: Homo_sapiens_assembly38.dbsnp138.vcf
  wgs_calling_interval_list: wgs_calling_regions.hg38.interval_list
  wgs_coverage_interval_list: wgs_coverage_regions.hg38.interval_list
  wgs_evaluation_interval_list: wgs_evaluation_regions.hg38.interval_list
  contamination_sites_bed: Homo_sapiens_assembly38.contam.bed
  contamination_sites_mu: Homo_sapiens_assembly38.contam.mu
  contamination_sites_ud: Homo_sapiens_assembly38.contam.UD