hello, , i have a snp typing file whose genotypes are in ATGC format that i want to convert to 0,1,2(Genotypes must be coded as dosage of allele 'b' 0, 1, 2.) your help is welcome Genotype calls: 0: A1A1 1: A1A2 or A2A1 2: A2A2 5: missing i use plink and my file is .csv format. is it possible to load files in .csv .txt format on plink
Okay, that's a good start. You appear to have enough information to create a PLINK object.
PLINK will not directly accept a CSV file, though. You will have to reformat your data to create a PED and MAP file, and then you will be able to create a PLINK object. Have you taken a look here:
To assist you, your PED file should have the following columns (but do not include these as a header - the file should be 'headerless'):
FID IID PID MID SEX PHENO
- FID, family ID
- IID, individual (sample) ID
- PID, paternal ID
- MID, maternal ID
- SEX, gender (1, male; 2, female)
- PHENO, phenotype (1, control; 2, case)
The information in this file can be space- or tab-delimited.
Your MAP file should have:
- Chromosome code (can be anything...)
- Variant identifier (e.g. SNP rs ID)
- Position in morgans or centimorgans (can just leave as 0)
- Base-pair coordinate
This can also be space- or tab-delimited.
If you then have both of these files, you can create a PLINK object with:
plink --file PlinkDataSet --ped MyData.tsv --map MyDataMap.tsv
If you only have the IID, then you can specify the following parameters along with the command (above), or choose one o more of these depending on what info you have:
--no-fid --no-parents --no-sex --no-pheno