Workflows V1

Workflows associated with version 1 of the Assay

BAM Generation & Quality Control

Overview of the BAM Generation and Quality Control workflow

Github Location -> https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/ACCESS_pipeline.cwl

Tools Used:

• BWA

• Trimgalore

• GATK

• Picard Tools

• ABRA2

• Marianas

Variant Calling

BAM files used for the workflows

Small Variants

Github Location -> https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/subworkflows/snps_and_indels.cwl

Tools Used:

• VardictJava

• MuTect

• VCF2MAF

Copy Number Variant (CNV)

Github Location -> https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/subworkflows/call_cnv.cwl

Refer to Bioinformatics Pipeline to Detect CNA's section in this paper for details:

Dara S. Ross, Ahmet Zehir, Donavan T. Cheng, Ryma Benayed, Khedoudja Nafa, Jaclyn F. Hechtman, Yelena Y. Janjigian, Britta Weigelt, Pedram Razavi, David M. Hyman, José Baselga, Michael F. Berger, Marc Ladanyi, Maria E. Arcila, Next-Generation Assessment of Human Epidermal Growth Factor Receptor 2 (ERBB2) Amplification Status: Clinical Validation in the Context of a Hybrid Capture-Based, Comprehensive Solid Tumor Genomic Profiling Assay, The Journal of Molecular Diagnostics, Volume 19, Issue 2, 2017, Pages 244-254, ISSN 1525-1578, https://doi.org/10.1016/j.jmoldx.2016.09.010.

Structural Variant (SV)

Github Location -> https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/subworkflows/manta.cwl

Tool Used:

• Manta

• iAnnotateSV

Microsatellite Instability Status (MSI)

Github Location -> https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/subworkflows/msi.cwl

Tool Used:

• ADMIE

Configurations

Voyager has all our configurations in the jinja template, it includes all the paths for various files and tools associated with the workflows, all location are on JUNO:

snps_indels: beagle/input_template.json.jinja2 at master · mskcc/beagle (github.com)

CNV: beagle/input_template.json.jinja2 at master · mskcc/beagle (github.com)

Fastq_to_bam: beagle/input_template.json.jinja2 at master · mskcc/beagle (github.com)

MSI: beagle/input_template.json.jinja2 at master · mskcc/beagle (github.com)

SV : beagle/input_template.json.jinja2 at master · mskcc/beagle (github.com)