vcf_rider

Library to efficiently compute score on individual genomes starting from vcf files

Documentation (ongoing!) here: https://vodkatad.github.io/vcf_rider/vcf_rider/index.html

Installation instructions

Install Rust (stable toolchain)

$ curl https://sh.rustup.rs -sSf | sh

(choose option 1 to install the stable toolchain by default)

Configure PATH variables in your shell without needing a new login:

$ $HOME/.cargo/env

Clone vcf_rider repository and build all binaries

$ git clone https://github.com/vodkatad/vcf_rider.git

$ cd vcf_rider

Build the package in release mode:

$ cargo build --release

Binaries than can be found in ./target/release/: vcf_rider indel_stats gc_rider gc_counter

Test your installation

Small number of unit tests:

$ cargo test --lib

More extensive tests that compare outputs with some manually checked:

cargo build; cd examples; make; make clean;

To build doc in target/doc

$ cargo doc --no-deps

Build indel stats to check if you have regions with too many mutated indels

$ cargo build --release --bin indel_stats

Then:

$ ./target/release/indel_stats your_vcf.vcf your_bed.bed

will result in a tab delimited file with information about the overlap between regions and mutations of the given bed and vcf, respectively. The sixth column will have true for all the regions that right now are not correctly managed by vcf_rider, due to a huge number of indels, and should be removed from your analyses cause they will be given incorrect scores. Future releases will fix this limitation.