https://github.com/msk-access/uncollapsed_bam_generation

Workflow for making MSK-ACCESS standard binary alignment mapping file.
https://github.com/msk-access/uncollapsed_bam_generation

cfdna ctdna cwl cwl-workflow umi workflow

Last synced: 4 months ago
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Workflow for making MSK-ACCESS standard binary alignment mapping file.

• Host: GitHub
• URL: https://github.com/msk-access/uncollapsed_bam_generation
• Owner: msk-access
• License: other
• Created: 2019-06-18T17:21:08.000Z (almost 7 years ago)
• Default Branch: master
• Last Pushed: 2025-01-21T16:02:33.000Z (over 1 year ago)
• Last Synced: 2025-01-21T16:40:05.003Z (over 1 year ago)
• Topics: cfdna, ctdna, cwl, cwl-workflow, umi, workflow
• Language: Common Workflow Language
• Homepage: https://msk-access.gitbook.io/uncollapsed-bam-generation
• Size: 1.83 MB
• Stars: 0
• Watchers: 3
• Forks: 2
• Open Issues: 6
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
---

description: >-

  CWL Workflow for producing genomic alignment files (BAM) from

  compressed FASTQ files having unique molecular index

---

# Un-collapsed Binary Alignment Map (BAM) file Generation

![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 \([https://www.commonwl.org/v1.0/](https://www.commonwl.org/v1.0/)\) 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's with unique molecular index(UMI), from Illumina sequencing data, but may be 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](./docs/.gitbook/assets/uncollapsed_bam_generation.png)