Skip to content
master
Go to file
Code

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
src
 
 
 
 
 
 
 
 
 
 
 
 

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.

About

VCFaid: Genotype likelihood based GQ estimation

Resources

License

Releases

No releases published

Packages

No packages published
You can’t perform that action at this time.