family.md

family.wdl inputs and outputs

• family.wdl inputs and outputs
  • DAG (simplified)
  • Inputs
    • Family Struct
    • Sample Struct
  • Outputs
    • Alignments, Coverage, and QC
    • Small Variants (<50 bp)
    • Structural Variants (≥50 bp)
    • Copy Number Variants (≥100 kb)
    • Tandem Repeat Genotyping
    • Variant Phasing
    • Variant Calling in Dark Regions
    • 5mCpG Methylation Calling
    • PGx Typing
    • Tertiary Analysis

DAG (simplified)

---
title: family.wdl
---
flowchart TD
  subgraph "`**Upstream of Phasing (per-sample)**`"
    subgraph "per-movie"
      ubam[/"HiFi uBAM"/] --> pbmm2_align["pbmm2 align"]
      pbmm2_align --> pbsv_discover["PBSV discover"]
    end
    pbmm2_align --> merge_read_stats["merge read statistics"]
    pbmm2_align --> samtools_merge["samtools merge"]
    samtools_merge --> mosdepth["mosdepth"]
    samtools_merge --> paraphase["Paraphase"]
    samtools_merge --> hificnv["HiFiCNV"]
    samtools_merge --> trgt["TRGT"]
    samtools_merge --> trgt_dropouts["TR coverage dropouts"]
    samtools_merge --> deepvariant["DeepVariant"]
  end
  subgraph "`**Joint Calling**`"
    deepvariant --> glnexus["GLnexus (joint-call small variants)"]
    pbsv_discover --> pbsv_call["PBSV call"]
    glnexus --> split_glnexus["split small variant vcf by sample"]
    pbsv_call --> split_pbsv["split SV vcf by sample"]
  end
  subgraph "`**Phasing and Downstream (per-sample)**`"
    split_glnexus --> hiphase["HiPhase"]
    trgt --> hiphase
    split_pbsv --> hiphase
    hiphase --> bcftools_roh["bcftools roh"]
    hiphase --> bcftools_stats["bcftools stats\n(small variants)"]
    hiphase --> sv_stats["SV stats"]
    hiphase --> cpg_pileup["5mCpG pileup"]
    hiphase --> starphase["StarPhase"]
    hiphase --> pharmcat["PharmCat"]
    starphase --> pharmcat
  end
  subgraph " "
    hiphase --> merge_small_variants["bcftools merge small variants"]
    hiphase --> merge_svs["bcftools merge SV"]
    hiphase --> trgt_merge["trgt merge"]
  end
  subgraph "`**Tertiary Analysis**`"
    merge_small_variants --> slivar_small_variants["slivar small variants"]
    merge_svs --> svpack["svpack filter and annotate"]
    svpack --> slivar_svpack["slivar svpack tsv"]
  end

Loading

Inputs

Type	Name	Description	Notes
Family	family	Family struct describing samples, relationships, and unaligned BAM paths	below
File	ref_map_file	TSV containing reference genome file paths; must match backend
String?	phenotypes	Comma-delimited list of HPO terms.	Human Phenotype Ontology (HPO) phenotypes associated with the cohort. If omitted, tertiary analysis will be skipped.
File?	tertiary_map_file	TSV containing tertiary analysis file paths and thresholds; must match backend	AF/AC/nhomalt thresholds can be modified, but this will affect performance. If omitted, tertiary analysis will be skipped.
Int?	glnexus_mem_gb	Override GLnexus memory; optional
Int?	pbsv_call_mem_gb	Override PBSV call memory; optional
Boolean	gpu	Use GPU when possible Default: false	GPU support
String	backend	Backend where the workflow will be executed ["GCP", "Azure", "AWS-HealthOmics", "HPC"]
String?	zones	Zones where compute will take place; required if backend is set to 'AWS' or 'GCP'.	Determining available zones in GCP
String?	gpuType	GPU type to use; required if gpu is set to true for cloud backends; must match backend	Available GPU types
String?	container_registry	Container registry where workflow images are hosted. Default: "quay.io/pacbio"	If omitted, PacBio's public Quay.io registry will be used. Custom container_registry must be set if backend is set to 'AWS-HealthOmics'.
Boolean	preemptible	Where possible, run tasks preemptibly [true, false] Default: true	If set to true, run tasks preemptibly where possible. If set to false, on-demand VMs will be used for every task. Ignored if backend is set to HPC.

Family Struct

The Family struct contains the samples for the family. The struct has the following fields:

Type	Name	Description	Notes
String	family_id	Unique identifier for the family	Alphanumeric characters, periods, dashes, and underscores are allowed.
Array[Sample]	samples	Sample struct with sample specific data and metadata.	below

Sample Struct

The Sample struct contains sample specific data and metadata. The struct has the following fields:

Type	Name	Description	Notes
String	sample_id	Unique identifier for the sample	Alphanumeric characters, periods, dashes, and underscores are allowed.
String?	sex	Sample sex ["MALE", "FEMALE", null]	Used by HiFiCNV and TRGT for genotyping. Allosome karyotype will default to XX unless sex is specified as "MALE". Used for tertiary analysis X-linked inheritance filtering.
Boolean	affected	Affected status	If set to true, sample is described as being affected by all HPO terms in phenotypes. If set to false, sample is described as not being affected by all HPO terms in phenotypes.
Array[File]	hifi_reads	Array of paths to HiFi reads in unaligned BAM format.
String?	father_id	sample_id of father (optional)
String?	mother_id	sample_id of mother (optional)

Outputs

Alignments, Coverage, and QC

Type	Name	Description	Notes
String	workflow_name	Workflow name
String	workflow_version	Workflow version
Array[String]	sample_ids	Sample IDs
File	stats_file	Table of summary statistics
Array[File]	bam_stats	BAM stats	Per-read length and read-quality
Array[File]	read_length_plot	Read length plot
Array[File]	read_quality_plot	Read quality plot
Array[File]	merged_haplotagged_bam	Merged, haplotagged alignments	Includes unmapped reads
Array[File]	merged_haplotagged_bam_index
Array[File]	mosdepth_summary	Summary of aligned read depth.
Array[File]	mosdepth_region_bed	Median aligned read depth by 500bp windows.
Array[File]	mosdepth_region_bed_index
Array[File]	mosdepth_depth_distribution_plot
Array[File]	mapq_distribution_plot	Distribution of mapping quality per alignment
Array[File]	mg_distribution_plot	Distribution of gap-compressed identity score per alignment
Array[String]	stat_num_reads	Number of reads
Array[String]	stat_read_length_mean	Mean read length
Array[String]	stat_read_length_median	Median read length
Array[String]	stat_read_quality_mean	Mean read quality
Array[String]	stat_read_quality_median	Median read quality
Array[String]	stat_mapped_read_count	Count of reads mapped to reference
Array[String]	stat_mapped_percent	Percent of reads mapped to reference
Array[String]	inferred_sex	Inferred sex	Sex is inferred based on relative depth of chrY alignments.
Array[String]	stat_mean_depth	Mean depth

Small Variants (<50 bp)

Type	Name	Description	Notes
Array[File]	phased_small_variant_vcf	Phased small variant VCF
Array[File]	phased_small_variant_vcf_index
Array[File]	small_variant_gvcf	Small variant GVCF	Can be used for joint-calling.
Array[File]	small_variant_gvcf_index
Array[File]	small_variant_stats	Small variant stats	Generated by bcftools stats.
Array[String]	stat_small_variant_SNV_count	SNV count	(PASS variants)
Array[String]	stat_small_variant_INDEL_count	INDEL count	(PASS variants)
Array[String]	stat_small_variant_TSTV_ratio	Ts/Tv ratio	(PASS variants)
Array[String]	stat_small_variant_HETHOM_ratio	Het/Hom ratio	(PASS variants)
Array[File]	snv_distribution_plot	Distribution of SNVs by REF, ALT
Array[File]	indel_distribution_plot	Distribution of indels by size
File?	joint_small_variants_vcf	Joint-called small variant VCF
File?	joint_small_variants_vcf_index

Structural Variants (≥50 bp)

Type	Name	Description	Notes
Array[File]	phased_sv_vcf	Phased structural variant VCF
Array[File]	phased_sv_vcf_index	Index for phased structural variant VCF
Array[String]	stat_sv_DUP_count	Structural variant DUP count	(PASS variants)
Array[String]	stat_sv_DEL_count	Structural variant DEL count	(PASS variants)
Array[String]	stat_sv_INS_count	Structural variant INS count	(PASS variants)
Array[String]	stat_sv_INV_count	Structural variant INV count	(PASS variants)
Array[String]	stat_sv_BND_count	Structural variant BND count	(PASS variants)
Array[File]	bcftools_roh_out	ROH calling	bcftools roh
Array[File]	bcftools_roh_bed	Generated from above, without filtering
File?	joint_sv_vcf	Joint-called structural variant VCF
File?	joint_sv_vcf_index

Copy Number Variants (≥100 kb)

Type	Name	Description	Notes
Array[File]	cnv_vcf	CNV VCF
Array[File]	cnv_vcf_index	Index for CNV VCF
Array[File]	cnv_copynum_bedgraph	CNV copy number BEDGraph
Array[File]	cnv_depth_bw	CNV depth BigWig
Array[File]	cnv_maf_bw	CNV MAF BigWig
Array[String]	stat_cnv_DUP_count	Count of DUP events	(for PASS variants)
Array[String]	stat_cnv_DEL_count	Count of DEL events	(PASS variants)
Array[String]	stat_cnv_DUP_sum	Sum of DUP bp	(PASS variants)
Array[String]	stat_cnv_DEL_sum	Sum of DEL bp	(PASS variants)

Tandem Repeat Genotyping

Type	Name	Description	Notes
Array[File]	phased_trgt_vcf	Phased TRGT VCF
Array[File]	phased_trgt_vcf_index
Array[File]	trgt_spanning_reads	TRGT spanning reads
Array[File]	trgt_spanning_reads_index
Array[File]	trgt_coverage_dropouts	TRGT coverage dropouts
Array[String]	stat_trgt_genotyped_count	Count of genotyped sites
Array[String]	stat_trgt_uncalled_count	Count of ungenotyped sites
File?	joint_trgt_vcf	Joint-called TRGT VCF
File?	joint_trgt_vcf_index

Variant Phasing

Type	Name	Description	Notes
Array[File]	phase_stats	Phasing stats
Array[File]	phase_blocks	Phase blocks
Array[File]	phase_haplotags	Per-read haplotag assignment
Array[String]	stat_phased_basepairs	Count of bp within phase blocks
Array[String]	stat_phase_block_ng50	Phase block NG50

Variant Calling in Dark Regions

Type	Name	Description	Notes
Array[File]	paraphase_output_json	Paraphase output JSON
Array[File]	paraphase_realigned_bam	Paraphase realigned BAM
Array[File]	paraphase_realigned_bam_index
Array[File?]	paraphase_vcfs	Paraphase VCFs	Compressed as .tar.gz

5mCpG Methylation Calling

Type	Name	Description	Notes
Array[File]	cpg_hap1_bed	CpG hap1 BED
Array[File]	cpg_hap1_bed_index
Array[File]	cpg_hap2_bed	CpG hap2 BED
Array[File]	cpg_hap2_bed_index
Array[File]	cpg_combined_bed	CpG combined BED
Array[File]	cpg_combined_bed_index
Array[File]	cpg_hap1_bw	CpG hap1 BigWig
Array[File]	cpg_hap2_bw	CpG hap2 BigWig
Array[File]	cpg_combined_bw	CpG combined BigWig
Array[String]	stat_cpg_hap1_count	Hap1 CpG count
Array[String]	stat_cpg_hap2_count	Hap2 CpG count
Array[String]	stat_cpg_combined_count	Combined CpG count

PGx Typing

Type	Name	Description	Notes
Array[File]	pbstarphase_json	PBstarPhase JSON	Haplotype calls for PGx loci
Array[File]	pharmcat_match_json	PharmCAT match JSON
Array[File]	pharmcat_phenotype_json	PharmCAT phenotype JSON
Array[File]	pharmcat_report_html	PharmCAT report HTML
Array[File]	pharmcat_report_json	PharmCAT report JSON

Tertiary Analysis

Type	Name	Description	Notes
File?	pedigree	Pedigree file in PLINK PED format
File?	tertiary_small_variant_filtered_vcf	Filtered, annotated small variant VCF
File?	tertiary_small_variant_filtered_vcf_index
File?	tertiary_small_variant_filtered_tsv	Filtered, annotated small variant calls
File?	tertiary_small_variant_compound_het_vcf	Filtered, annotated compound heterozygous small variant VCF
File?	tertiary_small_variant_compound_het_vcf_index
File?	tertiary_small_variant_compound_het_tsv	Filtered, annotated compound heterozygous small variant calls
File?	tertiary_sv_filtered_vcf	Filtered, annotated structural variant VCF
File?	tertiary_sv_filtered_vcf_index
File?	tertiary_sv_filtered_tsv	Filtered, annotated structural variant TSV