Hello!

I have a vcf file created by a bam file and another vcf file downloaded from ClinVar with all known variants with clinical significance. I have found the overlapping regions and I want to expand the annotation of the first file with the information from the second file (but I want to keep all the non pathological variants as well). Is there a function for this?

Thank you so much!

Lets say you have two VRanges x and y from readVcfAsVRanges(). Then, in the devel version of Bioconductor (3.4), you can do:

merge(x, y, all.x=TRUE)

There is no need to find overlaps upfront. The two variant sets will be matched by position and alt.