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66 bytes added, 11:38, 23 November 2013
= = is a small tool written in [[|Python]] to check input [ 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 [ rvtests] - rare-variant test software.
== Download ==
Download from [ this] and unzip the downloaded file. This includes [ ] script, reference genome in FASTA format and its index file.
== Example ==

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