Merging snpEff file and extracting novel mutations

Question

[realtreeecat]

Hi all, is there anyway to merge thousands of snpeff.vcf file and extract mutation that are novel or has mutilple occurrences in different nodes or is deeply penetrated into the phylogenetic tree? Is there any Python/R script for this.

How do i do this?

[Pierre Lindenbaum]

there anyway to merge thousands of snpeff.vcf

you asked bcftools merging 3540 individual files