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)
    • 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 "create fail_reads bait FASTA"
    trgt_catalog["TRGT catalog BED"]
    bait_fasta["create bait FASTA"]
  end
  subgraph "`**Upstream of Phasing\n(per-sample)**`"
    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"]
  end
  subgraph "`**Joint Calling**`"
    glnexus["GLnexus (joint-call small variants)"]
    sawfish_call["Sawfish call"]
    split_glnexus["split small variant vcf by sample"]
    split_sawfish["split SV vcf by sample"]
  end
  subgraph "`**Phasing and Downstream**`"
    hiphase["HiPhase"]
    samtools_merge_fail_reads["samtools merge hifi_reads and 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 " "
    merge_small_variants["bcftools merge small variants"]
    merge_svs["bcftools merge SV"]
    trgt_merge["trgt merge"]
  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 --> glnexus
  sawfish_discover --> sawfish_call

  glnexus --> split_glnexus
  sawfish_call --> split_sawfish
  split_glnexus --> hiphase
  split_sawfish --> 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 --> merge_small_variants
  hiphase --> merge_svs
  hiphase --> trgt_merge

  merge_small_variants --> slivar_small_variants
  merge_svs --> svpack
  svpack --> slivar_svpack

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 | max_reads_per_alignment_chunk | Maximum reads per alignment chunk

Default: 500000 | | | Int | pharmcat_min_coverage | Minimum coverage for PharmCAT

Default: 10 | | | Int | glnexus_mem_gb | GLnexus memory

Default: 60 | | | 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 | |

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. | | | 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. | | 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] | msg | Messages from the workflow | | | File | msg_file | File containing messages from the workflow | | | Array[String] | sample_ids | Sample IDs | | | File | stats_file | Table of summary statistics | | | Array[File] | bam_statistics | BAM statistics | Per-read length and read-quality | | Array[File] | read_length_plot | Distribution of read lengths | | | Array[File?] | read_quality_plot | Distribution of read qualities | | | 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 | Distribution of aligned read depth | | | Array[File] | mapq_distribution_plot | Distribution of mapping quality per alignment | | | Array[File] | mg_distribution_plot | Distribution of gap-compressed identity per alignment | | | Array[String] | stat_read_count | 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_length_n50 | Read length N50 | | | Array[String] | stat_read_quality_mean | Mean read quality | | | Array[String] | stat_read_quality_median | Median read quality | | | Array[String] | stat_mapped_read_count | Number of reads mapped to reference | | | Array[String] | stat_mapped_read_percent | Percent of reads mapped to reference | | | Array[String] | stat_gap_compressed_identity_mean | Mean gap-compressed identity | | | Array[String] | stat_gap_compressed_identity_median | Median gap-compressed identity | | | Array[String] | inferred_sex | Inferred sex | Sex is inferred based on relative depth of chrY alignments. | | Array[String] | stat_depth_mean | 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 statistics | Generated by bcftools stats. | | Array[String] | stat_small_variant_SNV_count | Number of SNVs | (PASS variants) | | Array[String] | stat_small_variant_INDEL_count | Number of INDELs | (PASS variants) | | Array[String] | stat_small_variant_TSTV_ratio | Ts/Tv ratio | (PASS variants) | | Array[String] | stat_small_variant_HETHOM_ratio | Het/Hom ratio for SNVs | (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 | Number of DUP structural variants | (PASS variants) | | Array[String] | stat_sv_DEL_count | Number of DEL structural variants | (PASS variants) | | Array[String] | stat_sv_INS_count | Number of INS structural variants | (PASS variants) | | Array[String] | stat_sv_INV_count | Number of INV structural variants | (PASS variants) | | Array[String] | stat_sv_BND_count | Number of BND structural variants | (PASS variants) | | Array[String] | stat_sv_SWAP_count | Number of structural variant sequence swap events | (PASS variants) | | File | sv_supporting_reads | Supporting reads for structural variants | | | Array[File] | sv_copynum_bedgraph | CNV copy number BEDGraph | | | Array[File] | sv_depth_bw | CNV depth BigWig | | | Array[File] | sv_gc_bias_corrected_depth_bw | CNV GC-bias corrected depth BigWig | | | Array[File] | sv_maf_bw | CNV MAF BigWig | | | Array[File] | sv_copynum_summary | CNV copy number summary JSON | | | Array[File] | bcftools_roh_out | Regions of homozygosity | bcftools roh | | Array[File] | bcftools_roh_bed | Regions of homozygosity BED | | | File? | joint_sv_vcf | Joint-called structural variant VCF | | | File? | joint_sv_vcf_index | | |

Mitochondrial variants and haplotypes

| Type | Name | Description | Notes | | ---- | ---- | ----------- | ----- | | Array[File] | mitorsaw_vcf | Mitochondrial variant VCF | | | Array[File] | mitorsaw_vcf_index | Index for mitochondrial variant VCF | | | Array[File] | mitorsaw_hap_stats | Mitochondrial haplotype statistics | |

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 | Aligned TRGT spanning reads | | | Array[File] | trgt_spanning_reads_index | | | | Array[File] | trgt_coverage_dropouts | TRGT regions with coverage dropouts | | | Array[String] | stat_trgt_genotyped_count | Number of sites genotyped by TRGT | | | Array[String] | stat_trgt_uncalled_count | Number of sites ungenotyped by TRGT | | | File? | joint_trgt_vcf | Joint-called TRGT VCF | | | File? | joint_trgt_vcf_index | | |

Variant Phasing

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

Variant Calling in Dark Regions

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

PGx Typing

| Type | Name | Description | Notes | | ---- | ---- | ----------- | ----- | | Array[File] | pbstarphase_summary | StarPhase summary | 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? | 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 | |