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overlapping read pairs in GATK 220.127.116.11
I came across this post regarding overlapping read pair: https://gatkforums.broadinstitute.org/gatk/discussion/1745/does-unifiedgenotyper-count-overlapping-paired-end-reads-as-two-separate-reads
I could not interpret the last comment by @ebanks. Could you explain me in terms of the new Haplotypecaller?