Hello
Now I am working with clinical human whole exome data after I got my vcf file from variant calling. I tested the snpeff to predict variant annotation but some variants got more than one annotation which was already described in the manual (https://pcingola.github.io/SnpEff/se_inputoutput/#multiple-annotations-per-vcf-line). I tried to fine-tune parameters to this java -jar -Xmx16g snpEff.jar -v -canon -ud 0 my.vcf > my.ann.vcf the result gave me only canonical transcript and downstream/ upstream interval size into zero but some variants still got multiple annotations (7% from the total number of variants). In the manual, they mentioned that they already sort the annotation according to Putative impact: Effects having a higher putative impact are first, Effect type: Effects assumed to be more deleterious effects first, Canonical transcript before non-canonical and Marker genomic coordinates (e.g. genes starting before first).
So it means that we can use the very first annotation of that variant, right?
Or any idea to choose the right annotation for clinical analysis
Thank you
JK
