VCFaid: Genotype likelihood based GQ estimation
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src added GQ to missing app Jun 16, 2017
.gitignore added GQ to missing app Jun 16, 2017
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Makefile
README.md

README.md

VCFaid installation (using recursive clone)

git clone --recursive https://github.com/tobiasrausch/vcfaid.git

cd vcfaid/

make all

VCFaid installation (using package manager)

Install Linux packages:

apt-get update

apt-get install -y build-essential g++ git cmake zlib1g-dev ant libbz2-dev libboost-date-time-dev libboost-program-options-dev libboost-system-dev libboost-filesystem-dev libboost-iostreams-dev

Install htslib:

git clone https://github.com/samtools/htslib.git

cd htslib && make && make lib-static && cd ..

Set environment variables for boost libraries and htslib:

export BOOST_ROOT=/usr

export SEQTK_ROOT=<htslib_path>

Build vcfaid:

git clone https://github.com/tobiasrausch/vcfaid.git

cd vcfaid/ && touch .htslib .boost && make all && cd ..

Running gq

./src/gq -g 30 -v output.vcf.gz input.vcf.gz

Running subset

Subset a VCF file to a list of sites and add INFO:SCORE for every selected site. Tab-delimited input bed file format (no header line): id score

./src/subset -b selected.bed -o selected.vcf.gz raw.vcf.gz

Credits

VCFaid takes quite a bit of actual code fragments from arfer.