github.com/PacificBiosciences/HiFi-human-WGS-WDL/HiFi-human-WGS-WDL-singleton

Le résumé fourni par la source

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 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 failed HiFi 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. | | Boolean | gpu | Use GPU when possibleDefault: 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? | 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 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 | | | 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_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_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 | Count 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 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 varian

Ce résumé expose les affirmations des auteurs. BNTIC ne l’interprète pas comme une validation indépendante des résultats.