---\ntitle: family.wdl\n---\nflowchart TD\n subgraph "`**Upstream of Phasing (per-sample)**`"\n subgraph "per-movie"\n ubam[/"HiFi uBAM"/] --> pbmm2_align["pbmm2 align"]\n pbmm2_align --> pbsv_discover["PBSV discover"]\n end\n pbmm2_align --> merge_read_stats["merge read statistics"]\n pbmm2_align --> samtools_merge["samtools merge"]\n samtools_merge --> mosdepth["mosdepth"]\n samtools_merge --> paraphase["Paraphase"]\n samtools_merge --> hificnv["HiFiCNV"]\n samtools_merge --> trgt["TRGT"]\n samtools_merge --> trgt_dropouts["TR coverage dropouts"]\n samtools_merge --> deepvariant["DeepVariant"]\n samtools_merge --> hiphase["HiPhase"]\n end\n subgraph "`**Joint Calling**`"\n deepvariant --> glnexus["GLnexus (joint-call small variants)"]\n pbsv_discover --> pbsv_call["PBSV call"]\n glnexus --> split_glnexus["split small variant vcf by sample"]\n pbsv_call --> split_pbsv["split SV vcf by sample"]\n end\n subgraph "`**Phasing and Downstream (per-sample)**`"\n split_glnexus --> hiphase\n trgt --> hiphase\n split_pbsv --> hiphase\n hiphase --> bcftools_roh["bcftools roh"]\n hiphase --> bcftools_stats["bcftools stats\\n(small variants)"]\n hiphase --> sv_stats["SV stats"]\n hiphase --> cpg_pileup["5mCpG pileup"]\n hiphase --> starphase["StarPhase"]\n hiphase --> pharmcat["PharmCat"]\n starphase --> pharmcat\n end\n subgraph " "\n hiphase --> merge_small_variants["bcftools merge small variants"]\n hiphase --> merge_svs["bcftools merge SV"]\n hiphase --> trgt_merge["trgt merge"]\n end\n subgraph "`**Tertiary Analysis**`"\n merge_small_variants --> slivar_small_variants["slivar small variants"]\n merge_svs --> svpack["svpack filter and annotate"]\n svpack --> slivar_svpack["slivar svpack tsv"]\n end\n| Type | Name | Description | Notes |\n| ---- | ---- | ----------- | ----- |\n| Family | family | Family struct describing samples, relationships, and unaligned BAM paths | below |\n| File | ref_map_file | TSV containing reference genome file paths; must match backend | |\n| String? | phenotypes | Comma-delimited list of HPO terms. | Human Phenotype Ontology (HPO) phenotypes associated with the cohort.
If omitted, tertiary analysis will be skipped. |\n| 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. |\n| Int? | glnexus_mem_gb | Override GLnexus memory; optional | |\n| Int? | pbsv_call_mem_gb | Override PBSV call memory; optional | |\n| Boolean | gpu | Use GPU when possible
Default: false | GPU support |\n| String | backend | Backend where the workflow will be executed["GCP", "Azure", "AWS-HealthOmics", "HPC"] | |\n| String? | zones | Zones where compute will take place; required if backend is set to 'AWS' or 'GCP'. | Determining available zones in GCP |\n| String? | gpuType | GPU type to use; required if gpu is set to true for cloud backends; must match backend | Available GPU types |\n| 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'. |\n| 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. |
The Family struct contains the samples for the family. The struct has the following fields:
| Type | Name | Description | Notes |\n| ---- | ---- | ----------- | ----- |\n| String | family_id | Unique identifier for the family | Alphanumeric characters, periods, dashes, and underscores are allowed. |\n| Array[Sample] | samples | Sample struct with sample specific data and metadata. | below |
\nThe Sample struct contains sample specific data and metadata. The struct has the following fields:
| Type | Name | Description | Notes |\n| ---- | ---- | ----------- | ----- |\n| String | sample_id | Unique identifier for the sample | Alphanumeric characters, periods, dashes, and underscores are allowed. |\n| 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. |\n| 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. |\n| Array[File] | hifi_reads | Array of paths to HiFi reads in unaligned BAM format. | |\n| String? | father_id | sample_id of father (optional) | |\n| String? | mother_id | sample_id of mother (optional) | |
| Type | Name | Description | Notes |\n| ---- | ---- | ----------- | ----- |\n| String | workflow_name | Workflow name | |\n| String | workflow_version | Workflow version | |\n| Array[String] | sample_ids | Sample IDs | |\n| File | stats_file | Table of summary statistics | |\n| Array[File] | bam_stats | BAM stats | Per-read length and read-quality |\n| Array[File] | read_length_plot | Read length plot | |\n| Array[File?] | read_quality_plot | Read quality plot | |\n| Array[File] | merged_haplotagged_bam | Merged, haplotagged alignments | Includes unmapped reads |\n| Array[File] | merged_haplotagged_bam_index | | |\n| Array[File] | mosdepth_summary | Summary of aligned read depth. | |\n| Array[File] | mosdepth_region_bed | Median aligned read depth by 500bp windows. | |\n| Array[File] | mosdepth_region_bed_index | | |\n| Array[File] | mosdepth_depth_distribution_plot | | |\n| Array[File] | mapq_distribution_plot | Distribution of mapping quality per alignment | |\n| Array[File] | mg_distribution_plot | Distribution of gap-compressed identity score per alignment | |\n| Array[String] | stat_num_reads | Number of reads | |\n| Array[String] | stat_read_length_mean | Mean read length | |\n| Array[String] | stat_read_length_median | Median read length | |\n| Array[String] | stat_read_quality_mean | Mean read quality | |\n| Array[String] | stat_read_quality_median | Median read quality | |\n| Array[String] | stat_mapped_read_count | Count of reads mapped to reference | |\n| Array[String] | stat_mapped_percent | Percent of reads mapped to reference | |\n| Array[String] | inferred_sex | Inferred sex | Sex is inferred based on relative depth of chrY alignments. |\n| Array[String] | stat_mean_depth | Mean depth | |
\n| Type | Name | Description | Notes |\n| ---- | ---- | ----------- | ----- |\n| Array[File] | phased_small_variant_vcf | Phased small variant VCF | |\n| Array[File] | phased_small_variant_vcf_index | | |\n| Array[File] | small_variant_gvcf | Small variant GVCF | Can be used for joint-calling. |\n| Array[File] | small_variant_gvcf_index | | |\n| Array[File] | small_variant_stats | Small variant stats | Generated by bcftools stats. |\n| Array[String] | stat_small_variant_SNV_count | SNV count | (PASS variants) |\n| Array[String] | stat_small_variant_INDEL_count | INDEL count | (PASS variants) |\n| Array[String] | stat_small_variant_TSTV_ratio | Ts/Tv ratio | (PASS variants) |\n| Array[String] | stat_small_variant_HETHOM_ratio | Het/Hom ratio | (PASS variants) |\n| Array[File] | snv_distribution_plot | Distribution of SNVs by REF, ALT | |\n| Array[File] | indel_distribution_plot | Distribution of indels by size | |\n| File? | joint_small_variants_vcf | Joint-called small variant VCF | |\n| File? | joint_small_variants_vcf_index | | |
| Type | Name | Description | Notes |\n| ---- | ---- | ----------- | ----- |\n| Array[File] | phased_sv_vcf | Phased structural variant VCF | |\n| Array[File] | phased_sv_vcf_index | Index for phased structural variant VCF | |\n| Array[String] | stat_sv_DUP_count | Structural variant DUP count | (PASS variants) |\n| Array[String] | stat_sv_DEL_count | Structural variant DEL count | (PASS variants) |\n| Array[String] | stat_sv_INS_count | Structural variant INS count | (PASS variants) |\n| Array[String] | stat_sv_INV_count | Structural variant INV count | (PASS variants) |\n| Array[String] | stat_sv_BND_count | Structural variant BND count | (PASS variants) |\n| Array[File] | bcftools_roh_out | ROH calling | bcftools roh |\n| Array[File] | bcftools_roh_bed | Generated from above, without filtering | |\n| File? | joint_sv_vcf | Joint-called structural variant VCF | |\n| File? | joint_sv_vcf_index | | |
| Type | Name | Description | Notes |\n| ---- | ---- | ----------- | ----- |\n| Array[File] | cnv_vcf | CNV VCF | |\n| Array[File] | cnv_vcf_index | Index for CNV VCF | |\n| Array[File] | cnv_copynum_bedgraph | CNV copy number BEDGraph | |\n| Array[File] | cnv_depth_bw | CNV depth BigWig | |\n| Array[File] | cnv_maf_bw | CNV MAF BigWig | |\n| Array[String] | stat_cnv_DUP_count | Count of DUP events | (for PASS variants) |\n| Array[String] | stat_cnv_DEL_count | Count of DEL events | (PASS variants) |\n| Array[String] | stat_cnv_DUP_sum | Sum of DUP bp | (PASS variants) |\n| Array[String] | stat_cnv_DEL_sum | Sum of DEL bp | (PASS variants) |
\n| Type | Name | Description | Notes |\n| ---- | ---- | ----------- | ----- |\n| Array[File] | phased_trgt_vcf | Phased TRGT VCF | |\n| Array[File] | phased_trgt_vcf_index | | |\n| Array[File] | trgt_spanning_reads | TRGT spanning reads | |\n| Array[File] | trgt_spanning_reads_index | | |\n| Array[File] | trgt_coverage_dropouts | TRGT coverage dropouts | |\n| Array[String] | stat_trgt_genotyped_count | Count of genotyped sites | |\n| Array[String] | stat_trgt_uncalled_count | Count of ungenotyped sites | |\n| File? | joint_trgt_vcf | Joint-called TRGT VCF | |\n| File? | joint_trgt_vcf_index | | |
\n| Type | Name | Description | Notes |\n| ---- | ---- | ----------- | ----- |\n| Array[File] | phase_stats | Phasing stats | |\n| Array[File] | phase_blocks | Phase blocks | |\n| Array[File] | phase_haplotags | Per-read haplotag assignment | |\n| Array[String] | stat_phased_basepairs | Count of bp within phase blocks | |\n| Array[String] | stat_phase_block_ng50 | Phase block NG50 | |
\n| Type | Name | Description | Notes |\n| ---- | ---- | ----------- | ----- |\n| Array[File] | paraphase_output_json | Paraphase output JSON | |\n| Array[File] | paraphase_realigned_bam | Paraphase realigned BAM | |\n| Array[File] | paraphase_realigned_bam_index | | |\n| Array[File?] | paraphase_vcfs | Paraphase VCFs | Compressed as .tar.gz |
| Type | Name | Description | Notes |\n| ---- | ---- | ----------- | ----- |\n| Array[File?] | cpg_hap1_bed | CpG hap1 BED | |\n| Array[File?] | cpg_hap1_bed_index | | |\n| Array[File?] | cpg_hap2_bed | CpG hap2 BED | |\n| Array[File?] | cpg_hap2_bed_index | | |\n| Array[File?] | cpg_combined_bed | CpG combined BED | |\n| Array[File?] | cpg_combined_bed_index | | |\n| Array[File?] | cpg_hap1_bw | CpG hap1 BigWig | |\n| Array[File?] | cpg_hap2_bw | CpG hap2 BigWig | |\n| Array[File?] | cpg_combined_bw | CpG combined BigWig | |\n| Array[String] | stat_cpg_hap1_count | Hap1 CpG count | |\n| Array[String] | stat_cpg_hap2_count | Hap2 CpG count | |\n| Array[String] | stat_cpg_combined_count | Combined CpG count | |
\n| Type | Name | Description | Notes |\n| ---- | ---- | ----------- | ----- |\n| Array[File] | pbstarphase_json | PBstarPhase JSON | Haplotype calls for PGx loci |\n| Array[File?] | pharmcat_match_json | PharmCAT match JSON | |\n| Array[File?] | pharmcat_phenotype_json | PharmCAT phenotype JSON | |\n| Array[File?] | pharmcat_report_html | PharmCAT report HTML | |\n| Array[File?] | pharmcat_report_json | PharmCAT report JSON | |
\n| Type | Name | Description | Notes |\n| ---- | ---- | ----------- | ----- |\n| File? | pedigree | Pedigree file in PLINK PED format | |\n| File? | tertiary_small_variant_filtered_vcf | Filtered, annotated small variant VCF | |\n| File? | tertiary_small_variant_filtered_vcf_index | | |\n| File? | tertiary_small_variant_filtered_tsv | Filtered, annotated small variant calls | |\n| File? | tertiary_small_variant_compound_het_vcf | Filtered, annotated compound heterozygous small variant VCF | |\n| File? | tertiary_small_variant_compound_het_vcf_index | | |\n| File? | tertiary_small_variant_compound_het_tsv | Filtered, annotated compound heterozygous small variant calls | |\n| File? | tertiary_sv_filtered_vcf | Filtered, annotated structural variant VCF | |\n| File? | tertiary_sv_filtered_vcf_index | | |\n| File? | tertiary_sv_filtered_tsv | Filtered, annotated structural variant TSV | |
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