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

Join Date: Mar 2012
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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
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Old 02-05-2013, 11:27 AM   #2
shoegame2001
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Default

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

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Default thank you

Quote:
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!
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