GDC MuSE

merge-muse:

muse-tool:

multi-muse:

MuSE is somatic point mutation caller developed by Dr. Wenyi Wang’s group in MD Anderson Cancer Center (MDACC), and used by the Human Genome Sequencing Center (HGSC) in the Baylor College of Medicine (BCM). Thus it is often referred to as the Baylor pipeline. This pipeline takes a pair of tumor and normal BAM files, and does two-step calling and summarization to generate somatic SNV and INDEL VCFs. The only auxiliary file requirement is a VCF file from Single Nucleotide Polymorphism Database (dbSNP) for annotation.

Original MuSE: http://bioinformatics.mdanderson.org/main/MuSE

How to build

https://docs.docker.com/engine/reference/builder/

The docker images are tested under multiple environments. The most tested ones are:

• Docker version 19.03.2, build 6a30dfc
• Docker version 18.09.1, build 4c52b90
• Docker version 18.03.0-ce, build 0520e24
• Docker version 17.12.1-ce, build 7390fc6

For external users

The repository has only been tested on GDC data and in the particular environment GDC is running in. Some of the reference data required for the workflow production are hosted in GDC reference files. For any questions related to GDC data, please contact the GDC Help Desk at support@nci-gdc.datacommons.io.

There is a production-ready CWL example at https://github.com/NCI-GDC/muse-cwl which uses the docker images that are built from the Dockerfiles in this repo.

To use docker images directly or with other workflow languages, we recommend to build and use either MuSE or multi-threading MuSE call.

To run multi-threading MuSE call:

docker run -it {YOUR DOCKER} muse_tool multi

or

python3.9 multi_muse.py

usage: Internal multithreading MuSE call. [-h] -f REFERENCE_PATH -r
                                          INTERVAL_BED_PATH -t TUMOR_BAM -n
                                          NORMAL_BAM -c THREAD_COUNT
                                          [--muse-binary MUSE_BINARY]

optional arguments:
  -h, --help            show this help message and exit
  -f REFERENCE_PATH, --reference_path REFERENCE_PATH
                        Reference path.
  -r INTERVAL_BED_PATH, --interval_bed_path INTERVAL_BED_PATH
                        Interval bed file.
  -t TUMOR_BAM, --tumor_bam TUMOR_BAM
                        Tumor bam file.
  -n NORMAL_BAM, --normal_bam NORMAL_BAM
                        Normal bam file.
  -c THREAD_COUNT, --thread_count THREAD_COUNT
                        Number of threads.
  --muse-binary MUSE_BINARY
                        Path to MuSE binary

For GDC users

See https://github.com/NCI-GDC/gdc-somatic-variant-calling-workflow.