I know there already are a lot of threads about this, but I still don't get it. I used ENSEMBL Release 98 for my analysis (variant calling) and I am now wondering what would have been the difference, if I had used a newer one.
If I understand this correctly, the underlying genome sequence (GRCh38.p13) is still the same and the different releases just have different annotations. And also the ENSEMBL Release number is not specific for the human genome, but for the whole ENSEMBL database.
Q0: Am I correct to this point? Q1: So, what is let's say the difference between GRCh38.p13 and GRCh38.p12?
I used BWA MEM to map reads to the reference genome.
Q2: If I use different ENSEMBL releases here, would the mapping differ? To my understanding this just depends on the sequence and not the annotation.
For a different analysis I filtered some genes from these BAM files with a BED file that I created from GENCODE v42. Could I do this or should I have used GENCODE v32 (or should GENCODE v42 still work regardless, of the ENSEMBL Release).
Q3: So, can someone tell me the difference, of the different releases? I still find the information available online a bit confusing.
Thanks for your help and patience :).