Combine multiple VCF files

HaploGrep2 currently accepts only single file uploads. To merge several VCF files to one, several tools exist:

CombineVariants
vcfcombine
vcf-merge

An example based on the VCFtools can be found here:

# For each VCF file:
bgzip Variants_sample_A.raw.vcf
tabix -p vcf Variants_sample_A.raw.vcf.gz

vcf-merge *.raw.vcf.gz >| Variants_all_samples.raw.vcf

Hope this helps!

 

hansi