How do I annotate known amino acid mutations like KRAS:G12C in a VCF?

Question

[nicola.calonaci]

Hi all,

is there any VEP-, snpEff- or annovar-like tool that you can use to automatically annotate known mutations as KRAS:G12C in a VCF file?

Suppose I have a VCF file with rows in the following format:

chr12   25393038    .   G   C   .   strand_bias CONTQ=6;DP=109;ECNT=1;GERMQ=93;MBQ=36,30;MFRL=366,534;MMQ=60,60;MPOS=37;NALOD=1.56;NLOD=10.23;POPAF=5.60;SEQQ=3;STRANDQ=1;TLOD=5.32;CSQ=C|intron_variant|MODIFIER|KRAS|ENSG00000133703|Transcript|ENST00000256078|protein_coding||2/5||||||||||-1||SNV|HGNC|6407|YES||||CCDS8703.1|ENSP00000256078|P01116|Q9UM97&Q71SP6&P78460&L7RSL8&I1SRC5|UPI0000133132|1||||||||||||||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|AC087239.1|ENSG00000268076|Transcript|ENST00000594112|protein_coding|||||||||||2198|1||SNV|Clone_based_ensembl_gene||YES|||||ENSP00000472051||M0R1Q5|UPI0001AE6A40||||||||||||||||||||||||||||||||| GT:AD:AF:DP:F1R2:F2R1:SB    0/1:65,3:0.060:68:35,2:26,1:42,23,0,3   0/0:36,0:0.027:36:20,0:15,0:26,10,0,0

I would need a tool that annotates this entry in the VCF with a column telling if the substitution is one of those with a known pathogenic effect like KRAS:G12C.

Any help is appreciated.

Answer 1

[a.v.vliet]

VEP allows you to do this with SIFT and PolyPhen: https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html (see Output options > --sift and --polyphen)