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Overview

The pipeline is written in Workflow Description Language (WDL), consisting of multiple modules to be executed in the following order.

  • GatherSampleEvidence SV evidence collection, including calls from a configurable set of algorithms (Manta, MELT, and Wham), read depth (RD), split read positions (SR), and discordant pair positions (PE).

  • EvidenceQC Dosage bias scoring and ploidy estimation.

  • GatherBatchEvidence Copy number variant calling using cn.MOPS and GATK gCNV; B-allele frequency (BAF) generation; call and evidence aggregation.

  • ClusterBatch Variant clustering

  • GenerateBatchMetrics Variant filtering metric generation

  • FilterBatch Variant filtering; outlier exclusion

  • GenotypeBatch Genotyping

  • MakeCohortVcf Cross-batch integration; complex variant resolution and re-genotyping; vcf cleanup

  • Module 07 (in development) Downstream filtering, including minGQ, batch effect check, outlier samples removal and final recalibration;

  • AnnotateVCF Annotations, including functional annotation, allele frequency (AF) annotation and AF annotation with external population callsets;

  • Module 09 (in development) Visualization, including scripts that generates IGV screenshots and rd plots.

  • Additional modules to be added: de novo and mosaic scripts

Pipeline Parameters​

Several inputs are shared across different modules of the pipeline, which are explained in this section.

ped_file​

A pedigree file describing the familial relationships between the samples in the cohort. The file needs to be in the PED format. Updated with EvidenceQC sex assignments, including sex = 0 for sex aneuploidies; genotypes on chrX and chrY for samples with sex = 0 in the PED file will be set to ./. and these samples will be excluded from sex-specific training steps.