# no_stats is essential if running through piped fh, or while loop never exits;
# port only used for offline mode (ensembl site); fork does not give sig. speed
# boost (16 sec for 880 row input with fork = 0 and fork = 4); fork _does_
# disrupt sort order of results; fork maybe causing script to hang occasionally;
# cache + offline uses local resource (/home/raj/.vep); force_overwrite required
# if output file already exists; sift, polyphen, check_existing, coding_only &
# regulatory params supplied from web form

#fork                2 # worse for dev - selectively enabled in VEP.pm
#core_type           core # can't find documentation for this opt

cache               1
dir                 /home/raj/.vep
force_overwrite     1
host                ensembldb.ensembl.org
no_stats            1
offline             1
output_file         stdout
port                5306
species             homo_sapiens
# needs full path to fasta file - vep.pl does: "die [...] unless -e $config->{fasta}"
fasta               /home/raj/.vep/fasta/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa