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Old 01-15-2013, 03:04 AM   #1
Junior Member
Location: barcelona

Join Date: Mar 2012
Posts: 2
Default vcf-merge EMPTY OUTPUT!

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
elecarnero is offline   Reply With Quote
Old 02-05-2013, 11:27 AM   #2
Location: California

Join Date: Dec 2010
Posts: 21

I had the same issue...using the "-p vcf" option when indexing with tabix solved it for me. Did you remember this?
shoegame2001 is offline   Reply With Quote
Old 01-14-2014, 11:52 AM   #3
Location: Rochester, NY

Join Date: Jan 2013
Posts: 43
Default thank you

Originally Posted by shoegame2001 View Post
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!
dGho is offline   Reply With Quote

combina, merge, vcftools

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