Fingerprinting

ListGenotypedVCFs

description
List all VCFs that have been genotyped

Inputs

Required

  • fingerprint_store (String, required): A bucket that holds all fingerprinting VCFs

Outputs

  • vcf_gs_paths (File)

PickGenotypeVCF

description
Pick a subset of VCFs that have been genotyped

Inputs

Required

  • fingerprinting_vcf_gs_paths (File, required): A file holding GS paths to fingerprinting GT'ed VCFs

Optional

  • vcf_name (String?): an expression used for picking up VCFs, the filter will be applied to VCF names, a match will lead to the VCF to be included

Outputs

  • vcfs (Array[String])

FilterGenotypesVCF

description
Filter out unwanted genotypes from a VCF

Inputs

Required

  • fingerprint_vcf (File, required): A VCF file that has been genotyped

Defaults

  • filters (Array[String], default=['_random\t', '_decoy\t', '_alt\t', '^chrUn', '^HLA', '^EBV']): An array of chromosome names to filter out when verifying fingerprints

Outputs

  • ready_to_use_vcf (File)

ExtractGenotypingSites

description
Extract genotyping sites from a VCF

Inputs

Required

  • fingerprint_vcf (File, required): A VCF file that has been genotyped

Outputs

  • sites (File)

MergeGenotypingSites

description
Merge genotyping sites from multiple VCFs

Inputs

Required

  • all_sites (Array[File], required): An array of genotyping sites

Outputs

  • merged_sites (File)

ExtractRelevantGenotypingReads

description
Based on genotyping (SNP) sites, extract reads that overlap those places

Inputs

Required

  • aligned_bai (File, required)
  • aligned_bam (File, required); localization_optional: true
  • genotyping_sites_bed (File, required)

Optional

  • runtime_attr_override (RuntimeAttr?)

Outputs

  • relevant_reads (File)
  • relevant_reads_bai (File)

ResetCLRBaseQual

description
Reset base quality scores to a fixed value

Inputs

Required

  • arbitrary_bq (Int, required): A fixed base quality score
  • bai (File, required): A BAI file
  • bam (File, required): A BAM file

Optional

  • runtime_attr_override (RuntimeAttr?)

Outputs

  • barbequed_bam (File)
  • barbequed_bai (File)

CheckFingerprint

description
Uses Picard tool CheckFingerprint to verify if the samples in provided VCF and BAM arise from the same biological sample

Inputs

Required

  • aligned_bai (File, required)
  • aligned_bam (File, required); description: GCS path to aligned BAM file, supposed to be of the same sample as from the fingerprinting VCF; localization_optional: true
  • fingerprint_vcf (File, required): Fingerprint VCF file from local database; note that sample name must be the same as in BAM
  • haplotype_map (File, required): Happlotype map file for the reference build used. See https://bit.ly/3QyZbwt
  • vcf_sample_name (String, required): Sample name in VCF, possibly different from that in the BAM.

Optional

  • runtime_attr_override (RuntimeAttr?)

Outputs

  • summary_metrics (File)
  • detail_metrics (File)
  • metrics_map (Map[String,String])

CheckCLRFingerprint

description
Uses Picard tool CheckFingerprint to verify if the samples in provided VCF and the CLR BAM arise from the same biological sample.

Inputs

Required

  • aligned_bai (File, required)
  • aligned_bam (File, required)
  • fingerprint_vcf (File, required)
  • haplotype_map (File, required): Haplotype map file for the reference build used. See https://bit.ly/3QyZbwt
  • vcf_sample_name (String, required): Sample name in VCF, possibly different from that in the BAM.

Optional

  • runtime_attr_override (RuntimeAttr?)

Defaults

  • min_base_q (Int, default=0)

Outputs

  • summary_metrics (File)
  • detail_metrics (File)
  • metrics_map (Map[String,String])

ReheaderFullGRCh38VCFtoNoAlt

desciption
Reheader the fingperint VCF that's generated with full GRCh38 reference to the no_alt header; project specific.

Inputs

Required

  • full_GRCh38_vcf (File, required): Full GRCh38 VCF file.

Outputs

  • reheadered_vcf (File)