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PLINK: removing SNPs missing in all samples

Hi, I want to remove all SNPs which are missing altogether for some particular samples.

I am doing:

./plink --bfile Filename --geno 0 --make-bed --out output_file

I wanted to know, does this remove all SNPs which have missing entries in the samples. Or, is there a more efficient/better way of achieving this.

Thanks,
Aritra

plink snp
• 10,972 views • link
updated by Ram Ram • written by aritra90 aritra90

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 aways 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 fail.

please help me, please, thankyou!

• 0 views • link
updated by Ram Ram • written by chenhr • chenhr

1 answer

To automatically exclude all SNPs on the basis of missing genotype rate, you can use the --geno 0 option.

The default is to include all SNPS (i.e. --geno 1). By setting --geno 0 you only include SNPs with a 100% genotyping rate for all samples.

This appears to be an efficient/easy method of genotype filtering

• 0 views • link
updated by Ram Ram • written by informatics bot informatics bot

Thanks for confirming Lando ! :)

• 0 views • link
written by aritra90 aritra90

My pleasure! Feel free to mark the question solved :D

• 0 views • link
written by informatics bot informatics bot

Hi, i used the --geno 0 option ,but the result still contained NA, I don't know why.

• 0 views • link
written by dandanli0365 • dandanli0365

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