Thank you for developing such a great tool. I have two variants called by mutect2, and I use annovar to annotate them, and I can't figure out why those coordinates didn't match.
Here is the information:
CHROM TYPE POS REF ALT AAChange
chr4 SNP 55593613 T C KIT:NM_000222:exon11:c.1679T>C:p.V560A,KIT:NM_001093772:exon11:c.1667T>C:p.V556A
chr4 INDEL 55593608 GGTT G KIT:NM_000222:exon11:c.1675_1677del:p.V560del,KIT:NM_001093772:exon11:c.1663_1665del:p.V556del
I wonder why that indel's HGVSc be position 560 in protein change? Shouldn't it be 559?
Thank you for developing such a great tool. I have two variants called by mutect2, and I use annovar to annotate them, and I can't figure out why those coordinates didn't match. Here is the information:
CHROM TYPE POS REF ALT AAChange chr4 SNP 55593613 T C KIT:NM_000222:exon11:c.1679T>C:p.V560A,KIT:NM_001093772:exon11:c.1667T>C:p.V556A chr4 INDEL 55593608 GGTT G KIT:NM_000222:exon11:c.1675_1677del:p.V560del,KIT:NM_001093772:exon11:c.1663_1665del:p.V556del
I wonder why that indel's HGVSc be position 560 in protein change? Shouldn't it be 559?