Hi there,
My genotype data only has 2 types and designed as 0 and 1 respectively (they are not in pairs format only give single number, and the third is ? represents missing), and i have no idea how could i arrange my ped file format as it requires 2 columns for each SNP. I tried when i set one column for each SNP, it indicated that the found columns less than expected. Is there anyone who can help me with this so i could arrange my genotype data to fit running format?
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kyc92dream •
You need an additional Map file. With that, plink should be able to convert your files automatically.
Example from Plink's own "toy" data:
(without header) CHR SNP-ID cM_Position(set to 0) BP_position
1 rs0 0 1000
1 rs10 0 1001
just create this file with a line for each of your markers and without the header, and it should work.
plink command example:
"plink --file INPUT --make-bed --out OUTFILE"
Plink will create a "binary" set of three files:
The map file will contain additional columns for your genotype alleles, coded with 0/1/2. You may later change that if you like, see "https://www.cog-genomics.org/plink/1.9/data#update_map"
Some additional tips:
I forgot something: You have to change the missing identifier (plink standard is "-9") or add the option "--missing-code ?" - but I am not sure, if plink is able to process the "?".
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Could you provide an example of your data?
0 H1 0 0 0 0.9 1 0 0 0 1 1 1 1 0
0 H2 0 0 0 2.3 0 0 0 0 1 1 1 0 0
0 H3 0 0 0 1.1 0 0 1 0 1 1 1 0 0
0 H4 0 0 0 1.1 0 0 0 0 1 1 1 0 0
0 H5 0 0 0 0.4 0 0 0 0 1 1 1 0 0
0 H6 0 0 0 1.1 0 0 0 0 1 0 1 0 0
I am doing quantitive trait study in crop, no family ID, parental ID and sex where i typed 0 under corresponding columns. SNP-based genotype data starts from 7th column(i only pasted 6 individuals and 9 SNPs here), one SNP takes one column.
And i tried to add flag compound-genotype, but it did not work as it should be 2 characters long.