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  • BAM Generation & Quality Control
  • Variant Calling
  • Small Variants
  • Copy Number Variant (CNV)
  • Structural Variant (SV)
  • Microsatellite Instability Status (MSI)
  • Configurations

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  1. The OnBoarding
  2. Computational Biologist
  3. MSK-ACCESS V1

Workflows V1

Workflows associated with version 1 of the Assay

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Last updated 3 years ago

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BAM Generation & Quality Control

Github Location ->

Tools Used:

Variant Calling

Small Variants

Tools Used:

Copy Number Variant (CNV)

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

Structural Variant (SV)

Tool Used:

Microsatellite Instability Status (MSI)

Tool Used:

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:

Github Location ->

Github Location ->

Github Location ->

Github Location ->

snps_indels:

CNV:

Fastq_to_bam:

MSI:

SV :

BWA
Trimgalore
GATK
Picard Tools
ABRA2
Marianas
https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/subworkflows/snps_and_indels.cwl
VardictJava
MuTect
VCF2MAF
https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/subworkflows/call_cnv.cwl
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.
https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/subworkflows/manta.cwl
Manta
iAnnotateSV
https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/subworkflows/msi.cwl
ADMIE
beagle/input_template.json.jinja2 at master · mskcc/beagle (github.com)
beagle/input_template.json.jinja2 at master · mskcc/beagle (github.com)
beagle/input_template.json.jinja2 at master · mskcc/beagle (github.com)
beagle/input_template.json.jinja2 at master · mskcc/beagle (github.com)
beagle/input_template.json.jinja2 at master · mskcc/beagle (github.com)
https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/ACCESS_pipeline.cwl
Overview of the BAM Generation and Quality Control workflow
BAM files used for the workflows
Page cover image