Can Plink2 read MacH dosage files

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Ake Lu

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Oct 21, 2015, 2:51:09 AM10/21/15
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Hi,

I have dosages files in MaCH/Minimac format and the annotation files including MAF estimates. I am wondering if PLINK2 can read the format then I can recalcuate the MAFs. The dosages were extracted from a subset of large sample while the MAFs were calculated based on the whole set. I need to re calculate the MAFs based on the subset but I cannot find the Plink commands that rad MaCH dosage files.

Thanks!

Ake

Christopher Chang

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Oct 22, 2015, 6:03:57 PM10/22/15
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Hi,

This is not directly supported by PLINK 1.9.  However, you can find a conversion script at https://www.genepi.qimr.edu.au/staff/sarahMe/dose2plink.html (note: the site's security certificate seems to be expired as of this writing); or if that runs out of memory, you can try compiling dose2plink.c under https://github.com/chrchang/plink-ng .

Ake Lu

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Oct 22, 2015, 6:23:34 PM10/22/15
to Christopher Chang, plink2-users

Thank you very much!

 

Best,

 

Ake

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Chao Xu

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Nov 14, 2016, 10:50:15 AM11/14/16
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Hi Christopher,

It's about the same question. The Minimac3 can make an dosage output in VCF format and Plink1.9 can take VCF as input. So I tried to read the VCF from Minimac3 into Plink and wrote it out in bed format. It worked. But I am not sure if it is appropriate doing this way? And I use gcta64 to convert the dosage to bed format. There are some differences in the map file. Some ref and alt alleles are flipped. I didn't check the differences of the haplotype in bed/ped. I am wondering could I use plink1.9 directly, just reading VCF from the Minimac3?

Thanks,
Chao

Christopher Chang

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Nov 14, 2016, 1:59:52 PM11/14/16
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If you need to keep ref/alt alleles, use plink's --keep-allele-order flag whenever you generate a new .bed/VCF file.

As for minimac3 -> .bed conversion, gcta64 is more convenient if you want to perform filtering on imputation r^2; otherwise gcta64 and plink should be equivalent.

Chao Xu

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Nov 14, 2016, 2:14:42 PM11/14/16
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OK. Clear now. Thanks!

MAOMAO

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Apr 14, 2020, 3:53:17 PM4/14/20
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Hi Christopher,

I was trying to use dose2plink.c under https://github.com/chrchang/plink-ng, but it gave me an error for line 7.  Any way to fix it? Thanks in advance.

./dose2plink.c -dose AFR.ATCG_chr10.phased_imputation.dose.gz -gz 0 -info AFR_combined_imputed.info -out AFR_chr10
./dose2plink.c: line 7: syntax error near unexpected token `newline'./dose2plink.c: line 7: `<!DOCTYPE html>'

Christopher Chang

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Apr 14, 2020, 3:55:34 PM4/14/20
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