I am using snpeff version 4.3t and have downloaded the database for hg19 to annotate my vcf files. However, the refseq version number of most transcripts seem to be a bit older and do not match with a list of transcript versions that is being used here in our lab (which was updated in july 2017 using UCSC table broswer). Is there a way to find out what refseq file is being used in snpeff ? Or is there a way to update it with refseq file that I have ?
I tried using the steps in here to update the data followed by
java -jar snpEff.jar build -refSeq -v hg19 but most of the links seem to be out of date and as a result building the database throws an error.
Can anyone suggest the steps to build the update-to-date refseq database for snpeff ?