hgvs annotation from VCF
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5 months ago
J.F.Jiang ▴ 880

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

VCF HGVS annotation • 248 views
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dups are insertions. code for such annotations is difficult.