| description |
|---|
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 standard processing workflow available here.
- Free software: Apache Software License 2.0
- Documentation: https://msk-access.gitbook.io/bam-collapsing
Given a uncollapsed Unique Molecular Index (UMI) tagged BAM file:
- Group Reads using UMI and generate a BAM file
- Call Duplex Consensus Reads from the BAM and generate an unmapped BAM file
- Convert unmapped BAM to FASTQ and do standard BAM alignment.
- Merge the unmapped BAM with the aligned BAM and this generated the collapsed BAM.
- Generate Duplex and Simplex BAM files from the collapsed BAM.
- CMO cfDNA Informatics Team
- This package was created with Cookiecutter and the
audreyr/cookiecutter-pypackageproject template.
