This is a simple rust application for counting the number of alt-reads and depths at locations provided in a 1-based region file. It works for CRAM and BAMs. This has not been tested extensively. This application was developed to call U2AF1 mutations in TOPMed for the Weinstock* & Gopakumar* et al., Nature, 2023 manuscript.
After running cargo build --release :
./target/release/pileup_region <region_file> <cram> <fasta>
The <region file> should have the following columns: chr, pos, ref, alt, aa_change . You
can leave aa_change as blank or a dummy value if you don't need it. The column headers need to
match these exactly.
An example file is provided here for the U2AF1 locus (u2af1_vars.txt) where the
coordinates are for GRCh38. Note that the genome build of this file must match that of the
BAM/CRAM.
The fasta file should be the same one used to align the BAM/CRAMs.
A pre-built Docker image is available at jweinstk/pileup_region on Docker Hub:
docker pull jweinstk/pileup_region
docker run -v /path/to/your/data:/data jweinstk/pileup_region pileup_region <region_file> <cram> <fasta>After cloning this repository, and installing the Rust programming language, run:
cargo build --release
It may take a few minutes to compile depending on your system.
Contact Josh Weinstock