Workflows V1

BAM Generation & Quality Control

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

Tools Used:

Variant Calling

Small Variants

Github Location ->

Tools Used:

Copy Number Variant (CNV)

Github Location ->

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

Structural Variant (SV)

Github Location ->

Tool Used:

Microsatellite Instability Status (MSI)

Github Location ->

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:

snps_indels:

CNV:

Fastq_to_bam:

MSI:

SV :