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Problem with validating resource bundle
I have been having trouble with the VCF files generated by GATK with either an error or warning when I run validate vcf saying that the reference allele is not matching. I went back an re downloaded the resource bundle from broad and ran validate VCF on the DBSNP vcf and get an error that "the REF allele is incorrect for the record at position 1:10054, fasta says CTA vs. VCF says CAA". I think that the troubles I have been having are due to a discrepancy between the various vcf files within the bundle.