Using tabix .csi index file to provide LD in locuszoom standalone

[rop....@gmail.com]

Dear locuszoom developers,

I'm intending to provide a vcf file while plotting in locuszoom standalone but I'm getting the error, "expected a tabix index for VCF file but could not find it" while I have the file with a .csi extension. I think it expects .tbi. Is there an option to specify this file so I can use the one with .csi extension.

Thanks,

Jesse

[Jesse Rop]

Dear locuszoom developers,

I have been able to solve this by using the .tbi accompanying the vcf. However, locuszoom seems to fail in calculating the LD from vcf "fileformat=VCFv4.2" giving the error .

"Error: while calculating LD from VCF file: index SNP position 157163395 does not exist in file.."

Thanks,

Jesse

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Jesse Rop

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[Sanjeev]

Were you able to solve this error?

I checked that the VCF file has SNP I am interested to plot for, but locuszoom errors out with message as yours.

[Jesse Rop]

Hi Sanjeev,

I wasn't able to solve this problem. I used the LD files provided with the standalone software. 

Best,

Jesse 

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