VerifyFingerprint

description: A workflow to check correctness of metadata on a flowcell, by genotyping it's BAM generated with its metadata, against a 'truth' genotyped VCF.

aligned_bai (File, required)
aligned_bam (File, required): GCS path to aligned BAM file, supposed to be of the same sample as from the fingerprinting VCF
collaborator_participant_id (String, required): Collaborator participant ID
collaborator_smid (String, required): Collaborator sample ID
expt_type (String, required): There will be special treatment for 'CLR' data (minimum base quality for bases used when computing a fingerprint)
fingerprint_store (String, required): GS path to where all known fingerprinting GT'ed VCFS are stored
gcs_out_root_dir (String, required): GCS bucket to store the reads, variants, and metrics files
ref_map_file (File, required): table indicating reference sequence and auxillary file locations
smid (String, required): SM- prefixed ID

artificial_baseQ_for_CLR (Int?): An artificial value for CLR reads used for fingerprint verification (CLR reads come with all 0 base qual)
use_this_fp_vcf (File?): Optional gt VCF, if provided, used for fingerprint verification (fingerprint_store, smid, collaborator_smid, collaborator_participant_id will all be ignored)
CheckCLRFingerprint.runtime_attr_override (RuntimeAttr?)
CheckFingerprint.runtime_attr_override (RuntimeAttr?)
ExtractRelevantGenotypingReads.runtime_attr_override (RuntimeAttr?)
FinalizeFingerprintDetailMetrics.keyfile (File?)
FinalizeFingerprintDetailMetrics.name (String?)
FinalizeFingerprintDetailMetrics.runtime_attr_override (RuntimeAttr?)
FinalizeFingerprintSummaryMetrics.keyfile (File?)
FinalizeFingerprintSummaryMetrics.name (String?)
FinalizeFingerprintSummaryMetrics.runtime_attr_override (RuntimeAttr?)
GetVCFSampleName.runtime_attr_override (RuntimeAttr?)
ResetCLRBaseQual.runtime_attr_override (RuntimeAttr?)

FilterGenotypesVCF.filters (Array[String], default=['_random\t', '_decoy\t', '_alt\t', '^chrUn', '^HLA', '^EBV'])

VerifyFingerprint