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How can I annotate specific alleles with dbSNP frequencies?

Dear all

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: 4.0.2.1, 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

Thank you!

Moreno

Answers

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @emmecola,

    VariantAnnotator calculates annotations based on the sample information within the VCF so your CAF value pertains to your VCF samples, not any dbSNP annotation.

    There is no simple way to obtain the results you need. If you will use GATK, one place to start is with CombineVariants. See this article for some pointers.

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