I wish to evaluate the quality score of my reads based on their distance from the start point of the read. I might see that after base X of the 101 bp, quality goes down. If it decreases very fast or even suddenly something went wrong in sequencing. Then I only want to look at maybe all the bases up to site X in my sequences.
Is there a way that GATK can do this and give me an average quality score based on position in the read?