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You require A different C++ program: prepareGenFromBeagle4. Obtain it from below. And compile it working with make. This application merges each of the VCFs produced by Beagle4 in action three and generates proper full chromosome input documents for SHAPEIT. A lot more specially, you have:

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This file should have N lines and 2L+6 columns, where N and L are definitely the numbers of individuals and SNPs contained in the dataset respectively. Every individual should have an special ID containing only alphanumeric characters. MAP file

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Every PIR is referred to as a line in this file. And each heterozyguous site coated is described by a triplet (index of your het from the map, allele observed, foundation excellent). As an example, the final PIR demonstrated In this particular file covers two hets: the 12th and also the 13th internet sites during the map with alleles G and T respectively, that were sequenced with foundation attributes 24 and 27. In this article, four critical factors need to be highlighted:

Monomorphic sites in PLINK Mattress format documents Will not now possess the alternate allele coded as 0, which means some incompatibility with Impute2.

As compared to a standard operate of SHAPEIT, not Substantially adjustments around the display other than this segment that describes how SHAPEIT made use of the PIRs presented:

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