I am running a GATK pipeline on RNA-seq data. For the alignment I have used GATK-bunle genome - human_g1k_v37_decoy.fasta. Now I would like to use the alignment files with featurecounts to obtain TPMs, which requires a GTF annotation file. However GATK bundle does not include annotation.
Which version of the annotation should I use? Will it be OK to use the latest version of the Ensembl annotation - GRCh37 release 87? Or should I go some versions down?