VCF file doesnt exit

[anujbio...@gmail.com]

Hi all,

I tried to run gwas in BLINK and my both files are myData.txt and myData.vcf. When I run a commond in BLINK, it shows error-

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*   BLINK v0.01 start   *
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*   BLINK is written by Meng Huang and designed by Zhiwu Zhang  *
*  Please visit zzlab.net to get more information about BLINK  *
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Input arguments:   --gwas --file --vcf
one cycle include 1000 SNPs inside!
The vcf genotype file doesn't exist!

The compressed binary files can't be created!

I just created a subset of my vcf file from a original vcf file using bcftools. is that be a prob?

Thanks

Anuj

[Meng Huang]

Hi Anuj,

The latest BLINK doesn’t support VCF and hapmap format. Now we recommend to use PLINK binary format as input file. 

Please try to use PLINK to convert VCF to plink binary file and downloads the new updated BLINK to run GWAS.

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