I am working with WES data for detection of somatic variants and I have used two variant callers because no variant caller is complete in itself. I have used GATK Haplotypecaller for small variants like snp,ins,del etc. And for large variants I have used pindel (specially for SVs detection). Now I have two vcf file for each patients, one from gatk and another from pindel. Although I know various vcf-merging tools but is it right to merge two different vcf file from different callers. Do they give right and proper merged vcf file. Are those vcf-merging tools SV-aware and consider only trivial call for the same variant represented differently in different callers. I know these are too many questions for a single thread but all these are related to each other. I am in dilemma whether I should merge them or use them separately.