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how can I recode phased haplotype?

Dear all

I have reconstructed haplotype from fastPHASE for each chromosome, as you know it has 0 /1 code, is there any way to recode it to A=1, C=2, G=3, T=4 by PLINK or any other software.

Any help will be appreciated

recode haplotype
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updated by Ram Ram • written by mary mary

Could you add sample output of fastPHASE?

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written by zx8754 zx8754

Hello,I got the same question,I think sweep needs the 1/2/3/4 code format,Have you found the way to solve the problem?Thank u.

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written by xgdong912 • xgdong912

2 answers

Output files for inferred haplotypes or imputed genotypes contain two lines per given diploid individual, with the order of individuals corresponding to that supplied in the input file. In addition, summary information is given, such as a recapitulation of some of the parameters from the fastPHASE run, and the command line supplied by the user. for example #IDA01 111110101010101010 100101011010100111 #IDA02 111111010101010101 111111111111111101 * * *
• 3 views • link
written by mary mary

SeqPHASE can be used for conversion

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written by evo_genomics • evo_genomics

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