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Reformat minimac imputated files to plink file

Hello all,

I am imputating my genotyped dataset, genotyped with illumina hapmap610 chip with minimac and mach according to standard protocols

I was wondering if anyone knows how to convert the output files of this imputation packages into standard plink format (ped and map files) with as side note that some filtering can be performed on the probability score that minimac gives as output.

Thanks in advance!

imputation minimac mach plink
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updated by Ram Ram • written by Floris Brenk Floris Brenk

I have met the same question !! Convert the .dos, .info formate of mimimac to the plink binary formate !! Have you solved that ??

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written by xujiayuan32257406 • xujiayuan32257406

I have met the same question !! Convert the .dos, .info formate of mimimac to the plink binary formate !! Have you solved that ??

• 0 views • link
written by xujiayuan32257406 • xujiayuan32257406

5 answers

Found it: http://www.complextraitgenomics.com/software/gcta/data_management.html

gcta64 --dosage-mach test.mldose.gz test.mlinfo.gz --make-bed --out test
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updated by Ram Ram • written by Floris Brenk Floris Brenk

I have tried gcta64, but the generated .bim formate didn't have the rsID, only the chr:bp position, still can't the following analysis? Do you know how to convert to the binary .bim formate?

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written by xujiayuan32257406 • xujiayuan32257406

Is it because the dose file does not have rsid? There is an option --rsid in Minimac3, which will use rsid instead of chr:bp in the output files including dose and info file.

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written by Xu1912 • Xu1912

I think dose2geno is the software you need.

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updated by Ram Ram • written by Maxime Lamontagne Maxime Lamontagne

I am wondering if you managed to figure out how to filter only high quality imputed genotypes from minimac3 output. I am struggling with the same problem you did. The dose2geno does provide best guess genotypes, but it does not seem to consider low quality scores. Using PLINKs vcf-min-gp flag is not working since plink expects 0-1 scale GP but minimac3 outputs phred scale. Any help would be highly appreciated if you managed to sort this!

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written by oyhel • oyhel

Hmm cant really remember how sorry, but I did filtered out all snps with a r2 score of lower than 0.3

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written by Floris Brenk Floris Brenk

Yes this looks indeed interesting. Although still a bit of reformatting needs to be done to get the actual .ped and .map files... One thing that still misses is that the probability score of the minimac output is not used now and I dont know what dose2geno does with imputed low probability scored genotypes...

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written by Floris Brenk Floris Brenk

Use fcgene to convert minimac output to PED/MAP files. You can also use rsq as filter:

fcgene --minimac-prob minimac_output.prob --minimac-infominimac_output.info --oformat plink --rsq 0.3 --out plink_files
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updated by Ram Ram • written by ISB • ISB

Thanks but fcgene requires pedinfo.txt and snpinfo.txt as input files. How can I prepare these 2 files using Minimac3 output files? And Minimac3 seems to not output .prob file.

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written by xliu4255 • xliu4255

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