Question

Fastphase To Plink Format

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11.7 years ago

kumar.vinod81 ▴ 340

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

plink format • 6.1k views

ADD COMMENT • link 11.7 years ago by kumar.vinod81 ▴ 340

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Can you give us sample output?

ADD REPLY • link 11.7 years ago by zx8754 12k

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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

ADD REPLY • link 11.7 years ago by kumar.vinod81 ▴ 340

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It not look like I want to paste here. SNP sites are row wise..

ADD REPLY • link 11.7 years ago by kumar.vinod81 ▴ 340

score 2 · Answer 1 · 2013-03-19

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11.7 years ago

zx8754 12k

The output looks like phased data, not imputed data. I suggest to use IMPUTE2

Convert plink files to gen format - use GTOOL
use IMPUTE2 for imputation
then use PLINK to work with dosage output

ADD COMMENT • link 11.7 years ago by zx8754 12k

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All the site are imputed but I am not able to convert them into PLINK format...I am completely failed.

ADD REPLY • link 11.7 years ago by kumar.vinod81 ▴ 340

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I've not used impute2. Is it easy to use?

ADD REPLY • link 11.7 years ago by kumar.vinod81 ▴ 340

score 2 · Answer 2 · 2013-03-21

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11.7 years ago

Wen.Huang ★ 1.2k

convert this format to plink's tped format, which is very similar to fastPHASE outputs, just a few extra columns
make a tfam file with the individual ID, etc.
with tped and tfam on hands, you can use plink to make various conversion if you need

ADD COMMENT • link 11.7 years ago by Wen.Huang ★ 1.2k

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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...

ADD REPLY • link 11.7 years ago by kumar.vinod81 ▴ 340

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Hi Kumar, did you ever find a solution to this? I am encountering the same problem....

ADD REPLY • link 10.9 years ago by 714 ▴ 110

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If you transpose your file, then it is similar to this question: Convert genotype matrix into plink format

ADD REPLY • link 10.9 years ago by zx8754 12k

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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

ADD REPLY • link 10.9 years ago by 714 ▴ 110

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See gtool -G option for GEN to PED Conversion mode.

ADD REPLY • link 10.9 years ago by zx8754 12k

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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

ADD REPLY • link 10.9 years ago by kumar.vinod81 ▴ 340