README.md

variant-summary-from-vcf

This is a utility to generate summary information about variants in an imputed VCF file. It assumes the VCF file has the following fields in its header:

• ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
• ##FORMAT=<ID=DS,Number=1,Type=Float,Description="Estimated Alternate Allele Dosage : [P(0/1)+2*P(1/1)]">
• ##FORMAT=<ID=GP,Number=3,Type=Float,Description="Estimated Posterior Probabilities for Genotypes 0/0, 0/1 and 1/1 ">

and so the format column will look like:

• GT:DS:GP

Building

To build the program, you will need LLVM 5.0. I built this project in a computing environment with

• GCC version 6.4.0-2.28
• LLVM version 5.0.1, most likely built specifically for GCC-6.4.0

You will also need the Haskell stack build tool, see installation instructions at:

• https://docs.haskellstack.org/en/stable/README/#how-to-install

After all that is installed, then run

• stack build
• stack install

Example of running the program on Linux

gzip -dc my_imputed.vcf.gz | ~/.local/bin/snp-summary-from-vcf-exe > snp_summary.tsv