singleton.md

singleton.wdl inputs and outputs

• singleton.wdl inputs and outputs
  • DAG (simplified)
  • Inputs
  • 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: singleton.wdl
---
flowchart TD
  subgraph "`**Upstream of Phasing**`"
    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"]
    pbsv_discover --> pbsv_call["PBSV call"]
  end
  subgraph "`**Phasing and Downstream**`"
    deepvariant --> hiphase["HiPhase"]
    trgt --> hiphase
    pbsv_call --> 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 "`**Tertiary Analysis**`"
    hiphase --> slivar_small_variants["slivar small variants"]
    hiphase --> svpack["svpack filter and annotate"]
    svpack --> slivar_svpack["slivar svpack tsv"]
  end

Loading

Inputs

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"]	Used by HiFiCNV and TRGT for genotyping. Allosome karyotype will default to XX unless sex is specified as "MALE".
Array[File]	hifi_reads	Array of paths to HiFi reads in unaligned BAM format.
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.
Boolean	gpu	Use GPU when possible Default: false	GPU support
String	backend	Backend where the workflow will be executed ["GCP", "Azure", "AWS-AGC", "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.

Outputs

Alignments, Coverage, and QC

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

Small Variants (<50 bp)

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

Structural Variants (≥50 bp)

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

Copy Number Variants (≥100 kb)

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

Tandem Repeat Genotyping

Type	Name	Description	Notes
File	phased_trgt_vcf	Phased TRGT VCF
File	phased_trgt_vcf_index
File	trgt_spanning_reads	TRGT spanning reads
File	trgt_spanning_reads_index
File	trgt_coverage_dropouts	TRGT coverage dropouts
String	stat_trgt_genotyped_count	Count of genotyped sites
String	stat_trgt_uncalled_count	Count of ungenotyped sites

Variant Phasing

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

Variant Calling in Dark Regions

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

5mCpG Methylation Calling

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

PGx Typing

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