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Revision as of 05:38, 5 August 2011
, 05:38, 5 August 2011→Convert Genotype Data to Build 37
After LiftOver, it is important to ensure that all genotypes are reported on the forward strand. This strand flipping can be facilitated by tools such as [http://pngu.mgh.harvard.edu/~purcell/plink/ PLINK] and [http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html GTOOL].
After LiftOver, it is important to ensure that all genotypes are reported on the forward strand. This strand flipping can be facilitated by tools such as [http://pngu.mgh.harvard.edu/~purcell/plink/ PLINK] and [http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html GTOOL].
== Convert Genotype Files Into IMPUTE format ==
After LiftOver to build 37 and ensuring that alleles are reported on the forward strand, you will have convert input files into IMPUTE format, one per chromosome. Before conversion, remember to sort SNPs by position because LiftOver from earlier genome builds can sometimes change marker order.
[http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html GTOOL] can be used to convert data from PLINK PED format to IMPUTE format.
= Pre-Phasing =
