Changes

= checkVCF.py =

= checkVCF.py =

checkVCF.py is a small tool written in [[www.python.org/|Python]] to check input [http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 VCF] files before association tests. It can report monomorphic sites, sites with reference alleles inconsistent with the reference genome, sites with invalid genotypes, non-SNP site (e.g. indels), and all sites with allele frequencies greater than ''0.5''. After you passed the checking, you can go on to run [https://github.com/zhanxw/rvtests rvtests] - rare-variant test software.

checkVCF.py is a small tool written in [http://www.python.org/ Python] to check input [http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 VCF] files before association tests. It can report monomorphic sites, sites with reference alleles inconsistent with the reference genome, sites with invalid genotypes, non-SNP site (e.g. indels), and all sites with allele frequencies greater than ''0.5''. After you passed the checking, you can go on to run [https://github.com/zhanxw/rvtests rvtests] - rare-variant test software.

== Download ==

== Download ==

Download from [http://www.sph.umich.edu/csg/zhanxw/software/checkVCF/checkVCF-20130223.tar.gz this] and unzip the downloaded file. This includes checkVCF.py script, reference genome in FASTA format and its index file.

Download from [http://www.sph.umich.edu/csg/zhanxw/software/checkVCF/checkVCF-20131123.tar.gz this] and unzip the downloaded file. This includes [https://github.com/zhanxw/checkVCF/blob/master/checkVCF.py checkVCF.py] script, reference genome in FASTA format and its index file.

== Example ==

== Example ==