plink remove snps with marker

Question

[chenhr]

Hello all

I want to used .ped and .map file to make population structure by frappe with a maximum likelihood method.first ,I used this command in plink: plink --ped DataResult.ped --recode12, then used this command in frappe: frappe MyParamSim.txt, but it always failed, the error as follow:

marker 664146 has only 2 non-missing alleles (8 required)
marker 664153 has only 2 non-missing alleles (8 required)
marker 664155 has only 4 non-missing alleles (8 required)
marker 664171 has only 2 non-missing alleles (8 required)
marker 664201 has only 2 non-missing alleles (8 required)
marker 664203 has only 6 non-missing alleles (8 required)
marker 664231 has only 2 non-missing alleles (8 required)
marker 664255 has only 2 non-missing alleles (8 required)
marker 664265 has only 6 non-missing alleles (8 required)
marker 664270 has only 6 non-missing alleles (8 required)
marker 664278 has only 4 non-missing alleles (8 required)
marker 664295 has only 6 non-missing alleles (8 required)
marker 664297 has only 6 non-missing alleles (8 required)
marker 664309 has only 6 non-missing alleles (8 required)
marker 664362 has only 6 non-missing alleles (8 required)

According to the error, I used this command in plink: plink --file DataResult.ped --geno 0.1, but it fails.

Please help me, please, thank you!

Answer 1

[Jimbou]

We can try

plink --file DataResult --geno 0.1 --recode --out subsetDataResult

[chenhr]

J

Thanks! I used this code, it's OK.

Thanks!

[chenhr]

I want to used frappe to construct population structure. I have ped and map file, I have used plink code :

plink --file DataResult --geno 0.1 --recode --out subsetDataResult

removed mirror as follows:

marker 664146 has only 2 non-missing alleles (8 required)
marker 664153 has only 2 non-missing alleles (8 required)
marker 664155 has only 4 non-missing alleles (8 required)
marker 664171 has only 2 non-missing alleles (8 required)
marker 664201 has only 2 non-missing alleles (8 required)
marker 664203 has only 6 non-missing alleles (8 required)
marker 664231 has only 2 non-missing alleles (8 required)
marker 664255 has only 2 non-missing alleles (8 required)
marker 664265 has only 6 non-missing alleles (8 required)
marker 664270 has only 6 non-missing alleles (8 required)
marker 664278 has only 4 non-missing alleles (8 required)
marker 664295 has only 6 non-missing alleles (8 required)
marker 664297 has only 6 non-missing alleles (8 required)
marker 664309 has only 6 non-missing alleles (8 required)
marker 664362 has only 6 non-missing alleles (8 required)--

but when I used frappe program，the mirror appeared again，as follows:

marker 333842 has only 4 non-missing alleles (8 required)
marker 333849 has only 6 non-missing alleles (8 required)
marker 333871 has only 6 non-missing alleles (8 required)
marker 333877 has only 2 non-missing alleles (8 required)
marker 333914 has only 6 non-missing alleles (8 required)
marker 333925 has only 2 non-missing alleles (8 required)
marker 333938 has only 0 non-missing alleles (8 required)
marker 333949 has only 2 non-missing alleles (8 required)
marker 333950 has only 0 non-missing alleles (8 required)
marker 333952 has only 2 non-missing alleles (8 required)
marker 333954 has only 4 non-missing alleles (8 required)
marker 333959 has only 4 non-missing alleles (8 required)

how to do it?

In other words, what files or data formats are required to build population structure, which one know, please tell me!

thanks!!