Make map file with recombination rate using plink?
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
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.
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.