How can I merge Multiple VCF files to have single header line

Question

[i.eberechi]

Hello Everyone,

I am working on VCF file format to upload them in an integrated platform. It demands that multiple entries of vcf file to be joined as a single file. I succeeded in doing that using vcftools along with bgzip and tabix tools for indeying and zipping. However, the merged file has several header and not one header..

Does anyone know how I may merge multiple VCF file to have only one header and not multiple(equivalent to the number of individual files)..

Thank you in advance..

[Jonathan Dursi]

I generally use vcfcombine from vcflib.

[i.eberechi]

ah thanks..i discovered the problem was the command i used. i had to include echo else the merged file will have an incorrect format. thanks for the answer.. at least i have an alternative option.

[Irsan]

have you tried vcf-merge?

[i.eberechi]

yes thanks it worked.