Workflows associated with version 1 of the Assay
Github Location -> https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/ACCESS_pipeline.cwl
Tools Used:
Github Location -> https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/subworkflows/snps_and_indels.cwl
Tools Used:
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:
Github Location -> https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/subworkflows/manta.cwl
Tool Used:
Github Location -> https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/subworkflows/msi.cwl
Tool Used:
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:
Things to know for MSK-ACCESS V1 for Research
It is a hybrid capture panel designed for Analysis of Circulating cfDNA to Evaluate Somatic Status using the Unique Molecular Index (UMIs) for high sensitivity. MSK-ACCESS is 13% as large, captures 47% of all mutations detected by MSK-IMPACT.
Selected exons of 129 genes for mutation detection
OncoKB Level 1-4
High rates of mutations
SNPs of zygosity & copy number of 12 genes
Common SNPs for genome-wide copy number
Introns for structural variants of 10 genes
Clonal hematopoiesis genes
Matched cfDNA-WBC (”tumor-normal”) assay to detect somatic alterations
Sensitivity for mutation calling depends on ‘duplex’ collapsed coverage
Different sensitivities for different classes of alterations
Genotyping +++++
De novo mutations, indels ++++
MSI +++
Rearrangements +++
Copy number ++
Tumor mutation burden ○
+ -> sensitivity for that event type
○ -> cannot be calculated