Merging files in plink

Question

[Tears]

Hello!

I am trying to merge files in plink, I used the following command:- ./plink --file data1 --merge data2.ped data2.map --noweb --recode --out merged. In my out file "merged file", some chromosomes are missing, which command can I use to merge files without losing data?

Thank you in advance

[Petr Ponomarenko]

do you get .missnp file and some kind of errors or warning from plink, maybe about triallelic sites? Try converting both data and data2 to bfiles (bed bim fam) and merge them using some other command like merge-list. Do you get the same results? Maybe you can share the files with us or at least a snippet with markers that are missing after merge?

[chrchang523]

plink assumes all distinct variants have different IDs; it tries to merge all variants with the same ID. Do you have entire chromosomes of variants named '.'?

[Leonida Monaco]

sorry for bothering you all. I am kind of having the same problem. I merged two dataset and it was ok. then I merged to this new file another dataset, and all went messed up. p value lower then 10e-200 very bad mind geno and maf result. the total of SNPs is more than 1 million but the common are 250000. the problem is that with merging these dataset I only obtained all of them in a big file. Is there a way to obtain b.file only with the common SNPs?

[stolarek.ir]

you can filter by the genotyping rate with the --geno flag

[Leonida Monaco]

yes I already did this, using geno mind and maf flag. but this only tells me that the SNPs quality is bad. There is a way to isolate all the common SNPs among these dataset?

Answer 1

[Tears]

Good day!

Thank you for your responses Petr Ponomarenko and chrchang523, my command is working. My mistake was not specifying that I'm working on a cow genome, I added --cow to my command and I got all my chromosomes. Thank you