I am working with some WES human data, I am trying to replicate some results from previous study from which I have the HGVS.c variants annotation and I need to get the genomic coordinates. I am doing pretty good with VEP but I found a couple of variants that are delins of 2 bases and resulted in splitted variants in my VCF file. As example:
NM_000179.2 MSH6 c.866_867delGCinsAA (Chr2: 48025988 - 48025989) p.Gly289Glu (clinvar page) is absent from my VCF but I have both:
2 48025988 rs368318845 G A 103592 PASS 0.0002592 1 A 2 48025989 rs267608047 C A 97356.5 PASS 0.0002393 1 A
that combined would result in the delGCinsAA above.
I am asking you, is there any simple method to "combine" these variants in order to know which patients are GC>AA hom, het and homref?
Thank you very much in advance for any help!