Question: convert .dose.gz and .info.gz files to plink binary format (.bim, .fam, .bed)
1
gravatar for jongyun.jung
4 weeks ago by
jongyun.jung10
USA
jongyun.jung10 wrote:

I have imputed data in the format of zipped as filename.dose.gz and info.gz.

1) I was wondering, how can I convert these files to plink binary format?

I used the software of dose2plink and then converted to .pfam and .pdat.gz files. However, I cannot figure out how to convert plink binary format from .pfam and .pdat.gz it. Here is the dose2plink webiste.

https://genepi.qimr.edu.au/staff/sarahme/dose2plink.html

2) Another question is to change the alleles (1/2/3/4) to the letter format (A/C/G/T). I know that I can use plink option of --alleleACGT. I was wondering, is it has to be in plink binary format to use this option?

http://www.cog-genomics.org/plink/1.9/data

--allele1234 interprets and/or recodes A/C/G/T alleles in the input as 1/2/3/4, while --alleleACGT does the reverse. With the 'multichar' modifier, these will translate multi-character alleles as well, e.g. "--allele1234 multichar" converts 'TT' to '44'.

Thank you for any help!

info plink imputation dose • 169 views
ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by jongyun.jung10
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