> For the complete documentation index, see [llms.txt](https://cmo-ci.gitbook.io/uncollapsed-bam-generation/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cmo-ci.gitbook.io/uncollapsed-bam-generation/develop-3/readme.md).

# Introduction

CWL Workflow for producing genomic alignment files (BAM) from compressed FASTQ files having unique molecular index

![GitHub Workflow Status (branch)](https://github.com/msk-access/uncollapsed_bam_generation/workflows/test_uncollapsed_bam_generation/badge.svg) [![Updates](https://pyup.io/repos/github/msk-access/uncollapsed_bam_generation/shield.svg)](https://pyup.io/repos/github/msk-access/uncollapsed_bam_generation/) [![Python 3](https://pyup.io/repos/github/msk-access/uncollapsed_bam_generation/python-3-shield.svg)](https://pyup.io/repos/github/msk-access/uncollapsed_bam_generation/)

This is the workflow is written using Common Workflow Language (CWL) version 1.0 (<https://www.commonwl.org/v1.0/>) and is used at Memorial Sloan Kettering Cancer Center for producing standard bam files from the NY state-approved MSK-ACCESS assay.

It is meant to be run on a single sample paired-end FASTQ with unique molecular index(UMI), from Illumina sequencing data, but maybe generalizable to other sequencing platforms and sequencing panels as well, which produce paired-end data with UMIs.

For documentation visit: <https://msk-access.gitbook.io/uncollapsed-bam-generation/>

![Workflow - Overview](https://3620429852-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-MJFLXsejYxzZQFC8q_n%2Fsync%2F3be3d46e88535ce4ac4985c96c661975140b8e68.png?generation=1607366076138470\&alt=media)