vcf-merge EMPTY OUTPUT!

[elecarnero]

Hello community,

I would like to merge different VCF files that contain genotype information of a single individual, in one single VCF file containing the information of all of them in different columns.

I am trying to do so by using vcf-merge command from VCFtools. The program seems to work fine when you have your vcf files zipped and indexed, and I do success in getting an vcf file output with each individual in a column of the header BUT the SNP list is completely EMPTY. The file ends in the header.

Any idea about why?

Thanks so much

[shoegame2001]

I had the same issue...using the "-p vcf" option when indexing with tabix solved it for me. Did you remember this?

[dGho]

thank you

I had the same issue...using the "-p vcf" option when indexing with tabix solved it for me. Did you remember this?

Thank you shoegame. I was having this problem too. Didn't realize we neede to use the -p option. This solved it for me!