Error: Same individual is twice in the data IBD command

[Théo]

Dear Pasi,

I am trying to use LepMap3 to construct a genetic map using a VCF file (created with STACKS) but unfortunately I am getting Errors when i am trying to use IBD tool.

I launched this command :

"java -cp lep_map3/lep_3/bin/ IBD data=urmiana_pedigree.txt vcfFile=vcf_urmiana_PL_GL.vcf numThreads=60 > ibd_urmiana-pedigree.txt"

And i have these error :

filtering markers...
Error 515
Error: Same individual is twice in the data

My pedigree files look like this : I have two parents mere-merged and pere-merged and all others individuals are son and daughters of them.

see file below

And i checked in my vcf i haven't twice individual

Any advice of how I can fix it?
Regards,
Théo

[Théo]

I also notice if i launch ParentCall2 with the same pedigree file and my vcf it's work !

So maybe IBD module doesn't like pedigree file because when i launch it with only the vcf it's work too.

Maybe i can use a parent file "parents=file:parents.txt" that i see in the option but i don't have example of this file. It is just a list of name of my parents ?

Thank for your answer

[Pasi Rastas]

Dear Théo,

Thank you for your question.

Just remove "data=..." parameter from the IBD and it should work.

Also note that IBD will take all markers from the vcf, probably a few thousand markers is enough (and much faster and uses less memory). So you could take only a subset of markers from the vcf for IBD.

Cheers,
Pasi