merging VCF files

[kjaja]

Hi all,

I need to merge multiple VCF files, any idea? I have tried it using VCFtools but it does not work. I get an error message
-bash: vcf-merge: command not found

thanks

[laura]

is your installation directory of vcftools in your $PATH env variable

[Dameon]

For many of the VCFtools, you also need to bgzip and tabix index VCf files. And Laura is correct, your installation of VCFtools should be in your $PATH env variable as well as exported to your PERL5LIB. It also wouldn't hurt to add bgzip and tabix as well. Just a word of warning though, some of the binary VCFtools do not work so well.
Alternatively, you could also try to use GATK to merge VCF files. You can find the necessary tool here:

http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_gatk_walkers_variantutils_CombineVariants.html

Good luck,
Dameon