I use the dbNSFP file locally and have downloaded it as described on the official website, sorted it and indexed it using Tabix. Now when I use the VEP command line tool offline with the dbNSFP plugin, I receive all the biologically possible variants and associated pathogenicity scores calculated cleanly for my gene.
However, when I retrieve the scores directly from the dbNSFP file using a tabix query without using the VEP script & dbNSFP plugin, certain chromosomal sections are missing. Do you have any suggestion what could be the reason for this?
I am using R for my direct query with the seqminer package and the following command:
tabix.read.table(file, position, col.names = TRUE, stringsAsFactors = FALSE)
„file" shows the path to my dbNSFP file and "position" gives the chromosome and the position on the chromosome.
Maybe there is a simple solution to my problem?
Thanks for your help!