Introduction

Collapsing of reads a aligned to the genome having same unique molecular identifier.

The bam collapsing workflow for MSK-ACCESS assay takes in a standard processed bam from the standard processing workflow available here.

• Free software: Apache Software License 2.0

• Documentation: https://msk-access.gitbook.io/bam-collapsing

Workflow

Features

Given an uncollapsed Unique Molecular Index (UMI) tagged BAM file:

1. Group Reads using UMI and generate a BAM file

2. Call Duplex Consensus Reads from the BAM and generates an unmapped BAM file

3. Convert unmapped BAM to FASTQ and do standard BAM alignment.

4. Merge the unmapped BAM with the aligned BAM and this generated the collapsed BAM.

5. Generate Duplex and Simplex BAM files from the collapsed BAM.

Credits

• CMO cfDNA Informatics Team

• This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.