hgvs annotation from VCF

Question

[J.F.Jiang]

Hi,

After variants calling, we used to use several tools, such as ANNOVAR, VEP, or SNPEff to annotate the vcf files.

However, annotations did not come to the right way as recommended in HGVS.p, especially those should be annotated as dup.

For example, variant 4 55593697 55593697 - ACTGAGTTTTGGTCTTCCTTATGATCACAAATGGGAGTTTCCCAGAAACAG

was converted to KIT:NM_000222:c.1763_1764insACTGAGTTTTGGTCTTCCTTATGATCACAAATGGGAGTTTCCCAGAAACAG:p.G592_K593insLPYDHKWEFPRNRLSFG, while it should be annotated as dup variation according to the latest recommendations, c.1727_1774+3dupTTCCTTATGATCACAAATGGGAGTTTCCCAGAAACAGGCTGAGTTTTGGTC/p.L576_G592dup

I am wondering any lite tool that can be applied to get the "right" hgvs annotation?

Thank, Junfeng

[cpad0112]

dups are insertions. code for such annotations is difficult.