Useful Resources

A large collection of resources

Bioinformatics-related:

Bcl2Fastq Docs, e.g. Illumina data description (including UMI & SampleSheet.csv details)

Bsub cheat sheet

Bsub Command usage

Bsub detailed usage

What are Read Groups?

SAM Format Spec

VCF format

Sam Flag Meanings (slide 30)

Quality Scores, ASCII

MSK HPC

IMPACT Pipeline

MSK Computing & Job Scheduling Docs

MSK Library

Cancer Hotspots

Berger Lab Publications

BCL2Fastq docs

MSKCC Platform Informatics readme

Bioinformatics lectures

NIH Cancer portal

LSF commands

MSKCC Luna docs

MSKCC hpc

GDC Cancer portal

GTex portal

Samtools tags

Software / ACCESS-related:

R style guide

Detailed Toil Documentation

Workflow Viewer (can be generated for any workflow in GitHub)

Common Workflow Language Documentation

CWL User Guide

CWL Reference Implementation

Toil Documentation

Toil Workflow Runner

Toil Development tickets

CWL in Vim

Innovation Manifest rules

PyUp.io dependency security checks