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Gatk Variantannotator not reannotating old rsIDs
I am trying to reannotate some .vcf produced using the miSeq pipeline using dbSNP version 137.
I am currently using VariantAnnotator to reannotate the called variants with the latest dbSNP version in order to ropvide the latest information on the called variants. I am currently using the following command:
PATH/TO/GATK -T VariantAnnotator -R path/to/hg19.fa --dbsnp dbSNP_147_hg19.vcf --variant starting.vcf -o final.vcf
As far as I understood, VariantAnnotator should remap the alleles and match them with the latest dbSNP, also removing rsIDs that were remapped to other locations compared to the dbSNP I'm using as reference. However, when I look at the final vcf, some rsIDs that were incorrectly reported during the miSeq Variant Calling are still there and often maps to different position compares to the ones stored in the latest dbSNP release.
A couple of examples:
In both my starting and final vcf rs41309540 is reported. It is found mapping on chrX:123042989 and represent the G/C allele. However, on the dbSNP official webiste, is reported at chrX:123909139 and represents the A/G switch. (source: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=41309540)
rs71646826 is reported by the miSeq pipeline to represent an A/C snp in chr1:240371085. However, when queried on the last dbSNP version, not only the alleles are different (A/T) but also its coordinates are different (chr1:240207785).
Am I using VariantAnnotator properly? If so, what is going on exactly? Should I remap the rsIDs using another tool instead?
Thanks a lot for your help!