expos

Statistically-backed VCF flagging calculating effect sizes and p-values for spatial properties of somatic mutations via Monte Carlo simulation and local reference complexity via Lempel-Ziv 76 method. Compares mutant reads with the set of all reads, including reads from one or more background-only samples.

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, bcftools RPBZ, amongst others.

Applicable to SNVs, small MNVs, and small indels.

High-performance implementation, adding minimal overhead to existing workflows.

---

Quick Start

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

# run
./expos my.vcf ref.fa my.bam > annotated.vcf

See Installation for full details and Usage for all options.