runVariant

run variant calling and filtering in a flexible way using GATK3 and plink Notes:

1. To run this package, in your PATH 'java1.8', 'samtools', 'bcftools', 'python' and 'parafly' are needed.
2. For python 'pandas' library is needed.
3. If those tools are not in your PATH, the package will automatically report an error!

Enjoy the testing!