Pipeline for merging vcf files from lumpy and cnvnator and sv filtering

Question

[nitinra]

Hello all,

I have obtained vcf output files from running lumpy and cnvnator. I am looking for a way/pipeline to merge vcf files from both these pipelines into one. Can I use the same tools that are used for SNPs (such as bedtools, bcftools) to merge these vcf files or is there a pipeline specific to CNVs? I am also looking for a pipeline that I can use to filter the concatenated vcf file to improve it's quality.

Thank you!