CMO Cell-Free DNA (cfDNA) Informatics Team

access_data_analysis

Scripts for downstream analysis plotting of pipeline output

biometrics

Python package to calculate various sample contamination metrics.

cwl-commandlinetools

Central location for CWL CommandLineTools

merge_fastq

Package to merge multiple pair of pair-end fastq data

nucleo

Workflow that creates all the BAM files for the cfDNA assay based FASTQ file at MSK

cwl_subworkflows

A list of subworkflows used for MSK-ACCESS data processing.

access_qc_generation

Generation Quality Controls Files for MSK-ACCESS

chip-var

Workflow for calling and annotating CHIP variants

genotype_variants

Project to genotype SNV, INDEL and SV.

nucleo_qc

Quality Control Workflow for UMI based BAMs

postprocessing_variant_calls

This repository helps with processing for variant calls made by a given caller

sequence_qc

Noise calculations from BAM file

access_artifacts

This repo tracts recurrent artifacts that we observe in MSK-ACCESS data

bam_collapsing

Workflow for collapsing of standard binary alignment mapping file generated by MSK-ACCESS

bcftools_1.15

copynumber_variation

cwl_pass_through

Blank CWL for Voyager Operators that don't use cwls.

DeltaMSI

DeltaMSI: AI-based screening for microsatellite instability in solid tumors

genomenexus

genomenexus_annotation-pipeline

microsatellite_instability

msisensor-ct

Microsatellite instability (MSI) detection for cfDNA samples.

msk-access.github.io

Documentation for MSK-ACCESS workflows

mskaccess_operators

Operators for creating input JSON using provided metadata

mutect1

picard

latest version of Picard tools from GATK (Broad Institute)

structural_variation

tabix-

uncollapsed_bam_generation

Workflow for making MSK-ACCESS standard binary alignment mapping file.

vardict-java