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


I wanted to use the program GERMLINE for the inference of IBD patterns and then DASH for the analysis ( 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 • 3.3k views
ADD COMMENTlink modified 5.3 years ago by arrow64110 • written 6.9 years ago by Tim10

Why not use Plink to calculate IBD?

ADD REPLYlink written 6.9 years ago by zx87548.9k
gravatar for arrow641
5.3 years ago by
United States
arrow64110 wrote:

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

ADD COMMENTlink written 5.3 years ago by arrow64110
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