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statgen / Minimac4

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Allowing chomosome number above 22 #27

Closed ChrisINRA closed 4 years ago

ChrisINRA commented 4 years ago

Hi, Thanks a lot for developing minimac4. I used Minimac2 few years ago and I'm impressed with the improvement in computing time.

Still, I have a minor problem. I'm working in cattle which have 29 chromosome (+ X and Y). I was able to convert my data to M3vcf files (using --chr option) but now I cannot run imputation for chromosome 23 and above.

"GWAS VCF File contains chromosome : 29 VCF File can only contain chromosomes 1-22, X(23), Y(24) !!! "

Is there an option to allow imputation on chromosome 29 for eg ?

Thanks in advance,

Chris

yukt commented 4 years ago

Hi Chris,

There is a latent option --MyChromosome in minimac4 that accommodates your needs. Please try adding "--MyChromosome 29” into your command line.

Best,

Ketian On Dec 19, 2019, 11:35 AM -0500, ChrisINRA notifications@github.com, wrote:

Hi, Thanks a lot for developing minimac4. I used Minimac2 few years ago and I'm impressed with the improvement in computing time. Still, I have a minor problem. I'm working in cattle which have 29 chromosome (+ X and Y). I was able to convert my data to M3vcf files (using --chr option) but now I cannot run imputation for chromosome 23 and above. "GWAS VCF File contains chromosome : 29 VCF File can only contain chromosomes 1-22, X(23), Y(24) !!! " Is there an option to allow imputation on chromosome 29 for eg ? Thanks in advance, Chris — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

ChrisINRA commented 4 years ago

It worked ! Thanks a lot. I looked twice on the doc but wasn't able to find the option.

Santy-8128 commented 4 years ago

Please use the hidden option --myChromosome 29 for it to work.

Regards, Sayantan Das,

23andMe

On Thu, Dec 19, 2019 at 8:35 AM ChrisINRA notifications@github.com wrote:

Hi, Thanks a lot for developing minimac4. I used Minimac2 few years ago and I'm impressed with the improvement in computing time.

Still, I have a minor problem. I'm working in cattle which have 29 chromosome (+ X and Y). I was able to convert my data to M3vcf files (using --chr option) but now I cannot run imputation for chromosome 23 and above.

"GWAS VCF File contains chromosome : 29 VCF File can only contain chromosomes 1-22, X(23), Y(24) !!! "

Is there an option to allow imputation on chromosome 29 for eg ?

Thanks in advance,

Chris

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