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!