Detect replication slippage variants at microsatellite regions

public 1yr ago Version: 1.0 0 bookmarks

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Snakemake workflow: bam-msisensor

This is a Snakemake workflow for microsatellite instability detection in bam files, powered by MSISensor .

Each tool belong to their authors.

See [wiki] for more information.

Rule Graph

workflow

Code Snippets

wrapper:
    f"{my_snw}/bio/cp"

SnakeMake From line 33 of rules/copy.smk

wrapper:
    f"{my_snw}/bio/cp"

SnakeMake From line 64 of rules/copy.smk

wrapper:
    f"{my_snw}/bio/cp"

SnakeMake From line 95 of rules/copy.smk

    wrapper:
        f"{swv}/bio/msisensor/scan"

"""
This rule scans both tumor and normal bam pairs in search for msi
More information at: https://github.com/ding-lab/msisensor
"""

SnakeMake From line 26 of rules/msisensor.smk

wrapper:
    f"{swv}/bio/msisensor/msi"

SnakeMake From line 80 of rules/msisensor.smk

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Created: 1yr ago

Updated: 1yr ago

Maitainers: public

URL: https://github.com/tdayris-perso/bam-msisensor

Name: bam-msisensor

Version: 1.0

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License: GNU General Public License v3.0

Keywords:

Data index Variant calling genetic variants MSI MSIsensor Snakemake microsatellite

Future updates

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