Building database with snpEff -- -gtf22 option not recognized/file not read

Question

[michael.dhar]

Hello!

I'm trying to create a custom database for snpEff. The documentation here (https://pcingola.github.io/SnpEff/snpeff/build_db/) calls for the option "-gtf22" before the name of the directory containing the GTF (and Fasta, etc). However, this option seems no longer to be recognized by snpEff, and I can't find the updated version in the documentation or in other queries. Without a "-gtf" option, the command produces an error stating that it can't read the input file (ie, the name of the directory containing the filies in the following command):

java -jar snpEff.jar build -v mm37.61

I get the same errors even doing their example build with the mouse database (with the latest mouse genome version used): mm39.114

java -jar snpEff.jar -c snpEff_dp-db-build-4-26-25.config build -gtf22 -v mm39.114

OR: without -gtf option: java -jar snpEff.jar -c snpEff_dp-db-build-4-26-25.config build -v mm39.114

Answer 1

[michael.dhar]

Based on the ordering of the commands here: https://github.com/pcingola/SnpEff/issues/583

I believe I just needed to place the "build" command before the config file specification.