Calculate statistics on VCF file with VCFtools

Description

Calculates several statistics on VCF files.

Parameters

• Report per-site frequency information (yes, no) [no]
• Report HWE p-value (yes, no) [no]
• Report LD statistics (yes, no) [no]
• Report SNP density (Integer) [0]

Details

Given a VCF file, calculates several statistics such as allele frequency and count, LD measure, and p-value for HWE (Hardy-Weinberg Equilibrium). It can also produce the number and density of SNPs in bins of defined size.

Output

Output is different reports (tsv and txt files).

References

This tool is based on the VCFtools package. Please cite the article The Variant Call Format and VCFtools by Danecek P., Auton A., Abecasis G, Albers C. A., Banks E., DePristo M. A., Handsaker R., Lunter G., Gabor Marth G., Sherry S. T., McVean G., Durbin R. and 1000 Genomes Project Analysis Group (2011) Bioinformatics, 27, 2156-8. [PMID: 21653522]