Stumbled on PLINK/SEQ while looking for a tool to estimate Ti/Tv from VCF files. At the moment, PLINK/SEQ seems limited to some older version of VCF, so it does not quite work with the files Goby generate (4.1), but I am interested in the mention of a binary file alternative to VCF, which could speed up some of the work we do (see section about project creation).
Tutorial: working with 1000 Genomes Pilot 3 VCFs. By way of introducing some of the features and approaches of PLINK/Seq, this page provides a tutorial that uses PSEQ and the R interface to PLINK/Seq …
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