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)
    • 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 "create fail_reads bait FASTA"
    trgt_catalog["TRGT catalog BED"]
    bait_fasta["create bait FASTA"]
  end
  subgraph "`**Upstream of Phasing**`"
    subgraph "per hifi_reads uBAM"
      ubam[/"HiFi uBAM"/]
      pbmm2_align["pbmm2 align"]
    end
    subgraph "per fail_reads uBAM"
      fail_ubam[/"fail reads uBAM (if provided)"/]
      bait_fail_reads["baited fail reads (if fail_reads provided)"]
      pbmm2_align_fail_reads["pbmm2 align baited fail_reads (if fail_reads provided)"]
      filter_fail_reads["filter fail_reads alignments (if fail_reads provided)"]
    end
    samtools_merge["samtools merge"]
    mosdepth["mosdepth"]
    paraphase["Paraphase"]
    mitorsaw["MitorSaw"]
    deepvariant["DeepVariant"]
    sawfish_discover["Sawfish discover"]
    sawfish_call["Sawfish call"]
  end
  subgraph "`**Phasing and Downstream**`"
    hiphase["HiPhase"]
    samtools_merge_fail_reads["samtools merge phased hifi_reads and aligned fail_reads"]
    trgt["TRGT"]
    bam_stats["BAM stats"]
    bcftools_roh["bcftools roh"]
    bcftools_stats["bcftools stats\n(small variants)"]
    sv_stats["SV stats"]
    cpg_pileup["5mCpG pileup"]
    methbat["MethBat"]
    starphase["StarPhase"]
    pharmcat["PharmCat"]
  end
  subgraph "`**Tertiary Analysis**`"
    slivar_small_variants["slivar small variants"]
    svpack["svpack filter and annotate"]
    slivar_svpack["slivar svpack tsv"]
  end

  trgt_catalog --> bait_fasta --> bait_fail_reads
  fail_ubam --> bait_fail_reads --> pbmm2_align_fail_reads --> filter_fail_reads --> samtools_merge_fail_reads
  ubam --> pbmm2_align --> samtools_merge
  samtools_merge --> mosdepth
  samtools_merge --> paraphase
  samtools_merge --> mitorsaw
  samtools_merge_fail_reads --> trgt
  samtools_merge --> deepvariant
  samtools_merge --> sawfish_discover
  samtools_merge --> hiphase
  deepvariant --> sawfish_discover
  deepvariant --> hiphase
  sawfish_discover --> sawfish_call --> hiphase

  hiphase --> trgt
  hiphase --> bam_stats
  hiphase --> bcftools_roh
  hiphase --> bcftools_stats
  hiphase --> sv_stats
  hiphase --> cpg_pileup
  hiphase --> starphase
  hiphase --> pharmcat
  hiphase --> trgt_dropouts
  starphase --> pharmcat
  cpg_pileup --> methbat

  hiphase --> slivar_small_variants
  hiphase --> svpack
  svpack --> slivar_svpack

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.
Array[File]?	fail_reads	Array of paths to fail_reads in unaligned BAM format (optional)	If provided, these reads will be aligned to the bait-captured regions.
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	max_reads_per_alignment_chunk	Maximum reads per alignment chunk Default: 500000
Int	pharmcat_min_coverage	Minimum coverage for PharmCAT Default: 10
Boolean	use_gpu	Use GPU when possible Default: false	GPU support
Boolean	use_parabricks_deepvariant	Use Parabricks DeepVariant implementation Default: false	If both use_parabricks_deepvariant and use_gpu are set to true, Parabricks DeepVariant will be used instead of standard DeepVariant. Parabricks DeepVariant
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 'GCP'	Determining available zones in GCP
String?	cpuPlatform	Minimum CPU platform to use for tasks on GCP	Optional, only necessary in certain zones lacking n1 nodes.
String?	gpuType	GPU type to use; required if use_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.
String?	debug_version	Debug version for testing purposes

Outputs

Alignments, Coverage, and QC

Type	Name	Description	Notes
String	workflow_name	Workflow name
String	workflow_version	Workflow version
Array[String]	msg	Messages from the workflow
File	msg_file	File containing messages from the workflow
File	stats_file	Table of summary statistics
File	bam_statistics	BAM statistics	Per-read length and read-quality
File	read_length_plot	Distribution of read lengths
File?	read_quality_plot	Distribution of read qualities
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	Distribution of aligned read depth
File	mapq_distribution_plot	Distribution of mapping quality per alignment
File	mg_distribution_plot	Distribution of gap-compressed identity per alignment
String	stat_read_count	Number of reads
String	stat_read_length_mean	Mean read length
String	stat_read_length_median	Median read length
String	stat_read_length_n50	Read length N50
String	stat_read_quality_mean	Mean read quality
String	stat_read_quality_median	Median read quality
String	stat_mapped_read_count	Number of reads mapped to reference
String	stat_mapped_read_percent	Percent of reads mapped to reference
String	stat_gap_compressed_identity_mean	Mean gap-compressed identity
String	stat_gap_compressed_identity_median	Median gap-compressed identity
String	inferred_sex	Inferred sex	Sex is inferred based on relative depth of chrY alignments.
String	stat_depth_mean	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 statistics	Generated by bcftools stats.
String	stat_small_variant_SNV_count	Number of SNVs	(PASS variants)
String	stat_small_variant_INDEL_count	Number of INDELs	(PASS variants)
String	stat_small_variant_TSTV_ratio	Ts/Tv ratio	(PASS variants)
String	stat_small_variant_HETHOM_ratio	Het/Hom ratio for SNVs	(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	Number of DUP structural variants	(PASS variants)
String	stat_sv_DEL_count	Number of DEL structural variants	(PASS variants)
String	stat_sv_INS_count	Number of INS structural variants	(PASS variants)
String	stat_sv_INV_count	Number of INV structural variants	(PASS variants)
String	stat_sv_BND_count	Number of BND structural variants	(PASS variants)
String	stat_sv_SWAP_count	Number of structural variant sequence swap events	(PASS variants)
File	sv_supporting_reads	Supporting reads for structural variants
File	sv_copynum_bedgraph	CNV copy number BEDGraph
File	sv_depth_bw	CNV depth BigWig
File	sv_gc_bias_corrected_depth_bw	CNV GC-bias corrected depth BigWig
File	sv_maf_bw	CNV MAF BigWig
File	sv_copynum_summary	CNV copy number summary JSON
File	bcftools_roh_out	Regions of homozygosity	bcftools roh
File	bcftools_roh_bed	Regions of homozygosity BED

Mitochondrial variants and haplotypes

Type	Name	Description	Notes
File	mitorsaw_vcf	Mitochondrial variant VCF
File	mitorsaw_vcf_index	Index for mitochondrial variant VCF
File	mitorsaw_hap_stats	Mitochondrial haplotype statistics

Tandem Repeat Genotyping

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

Variant Phasing

Type	Name	Description	Notes
File	phase_stats	Phasing statistics
File	phase_blocks	Phase blocks
File	phase_haplotags	Per-read phase assignment
String	stat_phased_basepairs	Number of basepairs within phase blocks
String	stat_phase_block_ng50	Phase block NG50

Variant Calling in Dark Regions

Type	Name	Description	Notes
File?	paraphase_summary	Paraphase summary
File?	paraphase_realigned_bam	BAM file of reads realigned by Paraphase
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	5mCpG haplotype 1 BED
File?	cpg_hap1_bed_index
File?	cpg_hap2_bed	5mCpG haplotype 2 BED
File?	cpg_hap2_bed_index
File?	cpg_combined_bed	5mCpG combined BED
File?	cpg_combined_bed_index
File?	cpg_hap1_bw	5mCpG haplotype 1 BigWig
File?	cpg_hap2_bw	5mCpG haplotype 2 BigWig
File?	cpg_combined_bw	5mCpG combined BigWig
String	stat_cpg_hap1_count	Number of scored reference 5mCpGs in haplotype 1
String	stat_cpg_hap2_count	Number of scored reference 5mCpGs in haplotype 2
String	stat_cpg_combined_count	Number of scored reference 5mCpGs combined
File?	methbat_profile	MethBat 5mCpG profile
String	stat_methbat_methylated_count	Number of profiled regions labeled as methylated
String	stat_methbat_unmethylated_count	Number of profiled regions labeled as unmethylated
String	stat_methbat_asm_count	Number of profiled regions labeled as having allele-specific methylation

PGx Typing

Type	Name	Description	Notes
File	pbstarphase_summary	StarPhase summary	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?	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 TSV
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 TSV
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