Dear all,

I'm using locateVariant function from "VariantANnotation" package. Here's what I do to get the txdb and process it's seqinfo():

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

keepStandardChromosomes(txdb)

newStyle <- mapSeqlevels(seqlevels(txdb), "NCBI")

txdb <- renameSeqlevels(txdb, newStyle)

dropSeqlevels(txdb, "MT")

Then I read in the VCF file:

vcf <- readVcf("/home/ali313/Documents/studies/master/umc-project/data/warm-up/archive/....vcf", "hg19") dropSeqlevels(vcf, "MT", pruning.mode = "coarse")

And after making sure the seqinfo() of both query and subject are identical I run: loc_all <- locateVariants(vcf2, txdb, AllVariants(), ignore.strand = T, asHits= T)

However, the number of hits that I get in return "2874" is more than the variants in VCF query "1530".

How could that be and what am I doing wrong?