Resource Annotation by Variant rather than Site
Posted in Ask the team | Last updated on 2012-12-11 02:31:16


Comments (5)

I would like to have certain annotations applied only if the variants in the resource and the target have the same genomic change. Ex: In Cosmic the following variants are present.

12      25398284        .       C       G       .       PASS    Genename=KRAS;MutationAA=p.G12A;MutationCDS=c.35G>C
12      25398284        .       C       A       .       PASS    Genename=KRAS;MutationAA=p.G12V;MutationCDS=c.35G>T
12      25398284        .       C       T       .       PASS    Genename=KRAS;MutationAA=p.G12D;MutationCDS=c.35G>A

However, in my VCF file I get the G12A annotation for all variants at this site even if the actual change is G12V or G12D.

Is this possible?


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