Pf7JointGenotyping

Pf7JointGenotyping.wdl Joint genotyping following the MalariaGEN Pf7 methods (pp.1-2): genome tiled in 10 kbp intervals (2,342 across 3D7 v3) per interval: GenomicsDBImport (-ip 500, --sample-name-map) -> GenotypeGVCFs 4.1.4.0 (--only-output-calls-starting-in-intervals --use-new-qual-calculator -L --annotation-group StandardAnnotation --annotation-group AS_StandardAnnotation) -> excise 500bp padding (SelectVariants -L ) gather -> VQSR (SNP & indel separate; train = Pf crosses 1.0 PASS, prior 15; -an QD -an FS -an SOR -an MQRankSum -an ReadPosRankSum, no DP/MQ; --maxGaussians 8) -> VQSLOD<2.0 filter in core -> merge core/non-core. Ingests the gVCFs produced by Pf7SingleSampleVariantCalling.wdl.

SCATTER WIDTH: the 2,342 intervals are BINNED into at most max_shards contiguous shards (default 10). Each shard task processes its intervals sequentially, so the fan-out is <=10 VMs, not 2,342. Contiguous binning keeps the intervals genome-ordered, so the final concat needs no re-sort.

Each task uses only tools present in its image: GATK tasks in the gatk image, VCF-wrangling (concat/filter/merge) in the bcftools image. Pf7 excised padding with bcftools view -r; we use gatk SelectVariants -L (equivalent) to keep the shard task in the gatk image. Pf7's final core/non-core merge used GATK3.8 CombineVariants; we use bcftools concat (documented divergence).

Pf7JointGenotyping

Inputs

Required

  • gvcf_indices (Array[File], required)
  • gvcfs (Array[File], required)

Defaults

  • bcftools_docker (String, default="us.gcr.io/broad-dsp-lrma/lr-basic:0.1.1")
  • cohort_name (String, default="pf7_cohort")
  • contigs_to_exclude (Array[String], default=["Pf3D7_API_v3", "Pf3D7_MIT_v3"])
  • core_bed (File, default="gs://broad-malaria-public/short_read_workspace_data/regions/regions-20130225.Core.bed")
  • gatk_docker (String, default="broadinstitute/gatk:4.1.4.0")
  • interval_pad (Int, default=500)
  • interval_size (Int, default=10000)
  • max_shards (Int, default=10)
  • pfcrosses_pass_vcf (File, default="gs://broad-malaria-public/short_read_workspace_data/ALL_CROSSES.sites_only.PASS.vcf.gz")
  • pfcrosses_pass_vcf_index (File, default="gs://broad-malaria-public/short_read_workspace_data/ALL_CROSSES.sites_only.PASS.vcf.gz.tbi")
  • ref_dict (File, default="gs://broad-malaria-public/short_read_workspace_data/reference/PlasmoDB-61_Pfalciparum3D7_Genome.dict")
  • ref_fasta (File, default="gs://broad-malaria-public/short_read_workspace_data/reference/PlasmoDB-61_Pfalciparum3D7_Genome.fasta")
  • ref_fasta_fai (File, default="gs://broad-malaria-public/short_read_workspace_data/reference/PlasmoDB-61_Pfalciparum3D7_Genome.fasta.fai")
  • vqslod_threshold (Float, default=2.0)
  • vqsr_max_gaussians (Int, default=8)
  • vqsr_prior (Float, default=15.0)
  • CreateSampleNameMap.disk_gb (Int, default=20)
  • CreateSampleNameMap.docker (String, default="us.gcr.io/broad-dsp-lrma/lr-basic:0.1.1")
  • CreateSampleNameMap.memory_gb (Int, default=3)
  • FilterMerge.disk_gb (Int, default=50)
  • FilterMerge.memory_gb (Int, default=8)
  • GatherVcfs.disk_gb (Int, default=50)
  • GenotypeShard.disk_gb (Int, default=100)
  • GenotypeShard.memory_gb (Int, default=10)
  • VQSRAnnotate.disk_gb (Int, default=50)
  • VQSRAnnotate.memory_gb (Int, default=16)

Outputs

  • cohort_genotyped_vcf (File)
  • cohort_genotyped_vcf_index (File)
  • cohort_filtered_vcf (File)
  • cohort_filtered_vcf_index (File)

Dot Diagram

Pf7JointGenotyping