Entering edit mode
5.8 years ago
yairgatt
▴
10
Hello all, I have recently been using the snpEff program to make predictions regarding the impact of different genomic variations in bacterial genomes. I have noticed that a few of my variations end up being annotated as "splice_region_variant" or "exon_loss_variant". This naturally seems quite odd as bacteria do not have splicing, exons or introns. The phenomenon does not seem to occur when running snpEff via the PATRIC variation analysis service, so I must assume that there are some parameters which will allow avoiding it, but I can't seem to find them. Does anyone have an idea?
Many thanks, Yair
Hello Yair, I think it's better to describe how you do and paste your command(code).
Hello Matthew, thank you for your reply! I am using it in different contexts, but for instance in order to annotate called SNPs from a Salmonella Typhimurium library I use snpEff version 4.1 with a line like:
java -Xmx4g -jar ${SNPEFF_PATH}/snpEff.jar -no-downstream -no-upstream Salmonella_enterica_serovar_Typhimurium_LT2_uid57799 $some_vcfHi i'm seeing the same result "splice_region_variant", did you found an answer ?