Hello I was tasked with merging the VCF files for annotation into one file for manta and/or cnvkit is there a command to do this or would In have to run the pipeline merge the individual vcf files into one and then annotate? From what I saw the merge command was only for the variant calling step and the annotated output for every other tool was individual by sample

Yes you wold need to do this manually merging is only implemented for SNV. If it is something that can be generalized, we are always happy to take contributions 😉