expos

Statistically-backed VCF flagging calculating effect sizes and p-values for spatial properties of somatic mutations via Monte Carlo simulation. Compares mutant reads (supporting observations) with the set of all reads (background), optionally including reads from a matched normal.

Useful for inspecting and flagging false positive variants caused by a variety of processes most commonly associated with a high number of PCR cycles. Builds on Ellis et al. 2021, GATK ReadPosRankSum, amongst others.

For both SNVs and small indels. MNV handling logic is present, but largely untested.

Alpha Software

Core functionality present but niceties and guard rails are not. Please report any bugs and ask any questions!

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Quick Start

# clone and build
git clone https://github.com/blex-max/expos-repo.git
cd expos-repo
mkdir build && cd build
cmake .. -DCMAKE_BUILD_TYPE=Release
cmake --build .

# run
./expos my.vcf my.bam

See Installation for full details and Usage for all options.