I've imputed my plink.ped file using fastPHASE. It was imputed successfully. But know I want to convert this fastPHASE file back into PLINK format. Any idea...
fastPHASE format (2 individuals and 11 SNPs, row wise mutation)
ID 5906291001R01C01 1 1 1 0 1 1 1 1 1 0 1 1 1 1 0 1 1 1 1 1 0 1
ID 5906291001R01C02 1 1 1 0 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1
All the site are imputed but I am not able to convert them into PLINK format...I am completely failed.
I've not used impute2. Is it easy to use?
Thanks Huang, but the SNP sites in fastPHASE format are in rows, not in subsequent columns. While in tped format, the SNP sites are in same row and different column. What to do? I am totally puzzled...
If you transpose your file, then it is similar to this question: Convert genotype matrix into plink format
I'm afraid the conversion is not that simple. The genotype for each individual is in rows. To use the example above:
The output of fastPHASE (2 individuals, 11 SNP loci)
ID 5906291001R01C01 1 1 1 0 1 1 1 1 1 0 1 1 1 1 0 1 1 1 1 1 0 1
ID 5906291001R01C02 1 1 1 0 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1
In short the format goes something like this for 3 SNP loci per individual:
SNP1_Allele_1 SNP2_Allele_1 SNP3_Allele_1 SNP1_Allele_2 SNP2_Allele_2 SNP3_Allele_2
I didnt get any reply from Biostar but one of my bioinformatician friend written a perl script, and now I am always to send data to him and he send me after its formatting.... But its really not simple with online available tools. Try to contact ur BI team.... Thanks
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Can you give us sample output?
fastPHASE format (2 individuals and 11 SNPs, row wise mutation) ID 5906291001R01C01 1 1 1 0 1 1 1 1 1 0 1 1 1 1 0 1 1 1 1 1 0 1 ID 5906291001R01C02 1 1 1 0 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1
It not look like I want to paste here. SNP sites are row wise..