Question: How To Prepare The Input For The Germline Software For The Inference Of Ibd Patterns
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gravatar for Tim
6.1 years ago by
Tim10
Tim10 wrote:

Hello

I wanted to use the program GERMLINE for the inference of IBD patterns and then DASH for the analysis (http://www1.cs.columbia.edu/~gusev/germline/). GERMLINE accepts PLINK input (.ped and .map) but the manual says that

Although the PLINK format is not intended for haplotypes, GERMLINE expects the respective alleles to appear in order; i.e. the first allele always corresponds to one haplotype and the second allele to the other. Also, PLINK arbitrarily re-orders the alleles in processing the files, so we do not recommend handling phased data with PLINK prior to GERMLINE analysis because the haplotypes may not be intact (use the -from_snp and -to_snp flags to target specific regions).

I have SNP array data in PLINK - do I have to do anything with them before running GERMLINE - or would I need to 'bin' different SNPs into an haplotype ?

plink • 3.0k views
ADD COMMENTlink modified 4.5 years ago by arrow64110 • written 6.1 years ago by Tim10
1

Why not use Plink to calculate IBD? http://pngu.mgh.harvard.edu/~purcell/plink/ibdibs.shtml

ADD REPLYlink written 6.1 years ago by zx87547.1k
0
gravatar for arrow641
4.5 years ago by
arrow64110
United States
arrow64110 wrote:

You can use gPLINK.JAR, right click your plink file and select open the files with Haploview.

ADD COMMENTlink written 4.5 years ago by arrow64110
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