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OpenSNP Height Prediction

OpenSNP


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How to use Plink?

Posted by Muhammad_Alfiansyah almost 2 years ago

any one knows how to convert genotype data to the training set formate?

Posted by David_Baranger  almost 2 years ago |  Quote

See https://www.cog-genomics.org/plink2 Example: plink –vcf genotyping_data_fullset_train.vcf.gz –recode A –out genotyping_data_fullset_train

1

Posted by Muhammad_Alfiansyah  almost 2 years ago |  Quote

Wow thank you!

I see you in the top, nice works!

Posted by SergeKrier  almost 2 years ago |  Quote

See https://www.cog-genomics.org/plink2 Example: plink –vcf genotyping_data_fullset_train.vcf.gz –recode A –out genotyping_data_fullset_train

Posted by SergeKrier  almost 2 years ago |  Quote

See https://www.cog-genomics.org/plink2 Example: plink –vcf genotyping_data_fullset_train.vcf.gz –recode A –out genotyping_data_fullset_train

not sure what’s I’m doing wrong but it fails :

./plink –-vcf genotyping_data_subset_test.vcf.gz –recode A –out genotyping_data_fullset_train PLINK v1.90b4.6 64-bit (15 Aug 2017) www.cog-genomics.org/plink/1.9/ (C) 2005-2017 Shaun Purcell, Christopher Chang GNU General Public License v3 Error: First parameter must be a flag. ««««««« For more information, try ‘plink –help [flag name]’ or ‘plink –help | more’.

Posted by Muhammad_Alfiansyah  almost 2 years ago |  Quote

Hi teraflops,

./plink.exe –vcf genotyping_data_subset_train.vcf –recode A –out genotyping_data_subset_train_2

The above command works just fine.

maybe you need to use – instead of –- ? The other diference is that i unzip the vcf file first.

Hope this helps!