This workflow represents the GATK Best Practices for SNP and INDEL calling on RNA-Seq data. Starting from an unmapped BAM file, it performs alignment to the reference genome, followed by marking duplicates, reassigning mapping qualities, base recalibration, variant calling and variant filtering. We used Broad’s best practice script in WDL format as a reference to create the BROAD Best Practices RNA-Seq Variant Calling 220.127.116.11 workflow in CWL version 1.0.
BROAD Best Practices Somatic CNV Panel Workflow is used for creating a panel of normals (PON) given a group of normal samples. Using read coverage collected over specified intervals, this workflow creates a panel of normals HDF5 file which is used in BROAD Best Practices Somatic CNV Pair Workflow for standardizing and denoising read counts. This workflow represents a CWL implementation of Broad’s best practice CNV panel WDL workflow.
BROAD Best Practices Somatic CNV Pair Workflow is used for detecting copy number variants (CNVs) as well as allelic segments. Given a tumor and optional matched normal sample, as well as panel of normals (PON) file, this workflow models and calls CNV segments. This workflow represents a CWL implementation of Broad’s best practice CNV pair WDL workflow.