Make map file with recombination rate using plink?
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9 weeks ago
curious ▴ 570

Trying to run germline and they use ped and map as input. They seem to have the 3rd map column for recombination rate not empty the example

if I convert a bfile to ped amd map:

plink --bfile filename --recode --tab --out myfavpedfile

the 3rd column of resulting map file for is all 0. I have not been able to get germline to work and I am starting to suspect it needs this 3rd column of the map file filled with values. How do I do this?

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btw, germline is old and slow and not really that accurate. It's much better to use something like hap-ibd https://www.sciencedirect.com/science/article/pii/S0002929720300525

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Thanks. Do you have any recommendations for relationship inference software that is not KING?

I am really looking to determine relationship status (parent offspring, full sibling, 2nd degree, 3rd degree) between members of a large cohort.

I have tried a few programs that feed into ERSA (germline, fastIBD) also trying raffi. Unfortunately some of these seem not really documented or difficult to get running.

I am trying to check output of KING against some other relationship inference program for troubleshooting.

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Why not use the inbuilt methods in plink2? https://www.cog-genomics.org/plink/2.0/distance#make_king should (probably) give you what you need. You can keep all your files in plink binary format as well.