Question: is it possible to know individual genotype(alleles) by SNP in plink?
1
gravatar for nayeona.hi
10 days ago by
nayeona.hi50
nayeona.hi50 wrote:

I made 3 binary files from MAP and PED files.
I'd like to know how to get individual genotypes per specific SNP.

When I open the .bim file, I just see the SNP and allele information but individual information (i.e. sample Id)

How to map the information?

I'd like to get information like this, and could open in Python or R.

Do I need some other tools for that? please let me know. For example,

SNP      SAMPLE     GENOTYPE 
rs53576    1111         AA
rs53576    1112         GA
rs53576    1113         GG
rs53576    1114         GA

Thank you in advance.

individual snp plink • 81 views
ADD COMMENTlink modified 4 days ago by zx87549.6k • written 10 days ago by nayeona.hi50
2
gravatar for Sam
5 days ago by
Sam3.1k
New York
Sam3.1k wrote:
plink --bfile <Bed file prefix> --extract <File contain SNP ID> --recode --out <name of output>

This should generate the desired output

ADD COMMENTlink written 5 days ago by Sam3.1k

I think they need --recode transpose.

ADD REPLYlink written 4 days ago by zx87549.6k
1

--recode will generate the ped file, which split the genotype into two columns. With --recode transpose you will get one variant per column, where the fifth and sixth fields are allele calls for the first sample in the .tfam file ('0' = no call); the 7th and 8th are allele calls for the second individual; and so on.

There are a large number of recode formats, maybe they can consult the manual page here https://www.cog-genomics.org/plink/1.9/data#recode

ADD REPLYlink written 3 days ago by Sam3.1k

--list and --snp options also worked. Thank you

ADD REPLYlink modified 3 days ago • written 3 days ago by nayeona.hi50
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