Somatic base substitution caller for LRS

Python tool that calls somatic base substitutions from matched tumour-normal whole genome pileups.

Required

Python 3.6+

Install

Install into a virtualenv is recommended, e.g.:

python3 -m venv SBSC
source SBSC/bin/activate
tempdir=$(mktemp -d)
git clone https://github.com/shimbalama/SBSC $tempdir
cd $tempdir
tox # run tests: this is optional and requires tox be installed
pip3 install -r requirements.txt .

Prerequisites

Tabix-indexed pileups from samtools. samtools mpileup should be run with the following options:

samtools mpileup \
    --fasta-ref [reference.fa] \
    --count-orphans \
    --no-BAQ \
    --max-depth 500 \
    --min-BQ 1 \
    --ignore-RG \
    --ignore-overlaps \
    -a -a \
    --output-BP \
    --output-MQ \
    --output-extra FLAG,QNAME \
    [bam] | bgzip > [pileup.gz]

tabix should be run with the following options:

tabix -b 2 -e 2 [pileup.gz]

When the tool runs .tbi index files are presumed to exist adjacent to input pileup files.

Running the program

# help
SBSCall.py --help

# basic example
SBSCall.py call \
    -r /path/to/reference \
    -c /path/to/cancer_pileup.gz \
    -n /path/to/normal_pileup.gz 

Authors

• Liam McIntyre - https://github.com/shimbalama/

License

This project is licensed under the MIT License. See LICENSE

Acknowledgments

QIMR Berghofer medical genomics team