I'm attempting to annotate SNPs from VCF files I have downloaded from the TCGA dataportal. I'm able to identify their locations, but when i try to use the predictCoding() "coding <- predictCoding(vcf,txdb,seqSource = Hsapiens)" to identify effect of the variants in the coding regions I get the following error
Error in .getOneSeqFromBSgenomeMultipleSequences(x, names[i], start[i], :
sequence ^1$ not found
Could someone suggest a work around or a way to fix the error.
the version of R i use is version.string R version 3.2.0 (2015-04-16), in case that makes a difference.