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How can I annotate specific alleles with dbSNP frequencies?
I would like to annotate a VCF file using dbSNP as a resource VCF, specifically I want to add the 1000 genomes frequency of the called alleles. I tried the VariantAnnotator tool using the --resource-allele-concordance option, but apparently it doesn't work the way I expected.
Check this variant, for example:
chr21 10602110 . T C
The tool correctly identifies the dbSNP variant rs150482, but it says dbSNP.CAF=0.1713 which is not the C allele frequency according to the dbSNP vcf (C=0.8287):
chr21 10602110 rs150482 T C . . RS=150482;RSPOS=10602110;dbSNPBuildID=79;SSR=0;SAO=0;VP=0x050300000a05150537000100;GENEINFO=TPTE:7179;WGT=1;VC=SNV;S3D;SLO;NSM;REF;ASP;VLD;G5;HD;GNO;KGPhase1;KGPhase3;CAF=0.1713,0.8287;COMMON=1
Can you please help me? Is there a way to obtain the result that I need?
I am using GATK version: 18.104.22.168, and this is my command line:
gatk VariantAnnotator -R GRCh38.p2.mask1.fasta -V input.vcf -O output.vcf --resource dbSNP:dbSNP_variants.vcf --resource-allele-concordance -E dbSNP.CAF