Suppose I have a list of genomic positions and a reference GTF/ GFF3. Are there any software tools (any language is fine) that maps the position to the cDNA/ CDS position in relate to any transcript(s) that it may overlap?
For example, based on hg38 and GENCODE version 25, I would expect an input of chr1:151406413 would give the following as output (using CDS coordinates): ENST00000271715: 2622, ENST00000368863: 2337, ENST00000392723: 2463, ENST00000409503: 2595, ENST00000491586: 2490, ENST00000529669: 822 and ENST00000531094: 2436.
I know I can just throw it into ANNOVAR or VEP; but I wonder if there's a simpler way without actually predicting the consequences.
Thanks anyone for the answer in advance!