MarkDuplicates vs. MarkduplicatesWithMateCigar: what is the best practice?
I am curious to know which tool (MarkDuplicates or MarkduplicatesWithMateCigar) would people advice for marking duplicates (I am following GATK's Best Practices from paired-end DNA reads). I get that MarkduplicatesWithMateCigar also uses CIGAR infos to mark them, but struggle justifying the supposed added value of using this tool vs. the "regular" MarkDuplicates.
Also, selecting representative nondups based on the total mapped length of a pair (ie, MarkduplicatesWithMateCigar method) rather than on the sum of base qualities of a pair (ie, Markduplicates method) seems more intuitive to me. Why would one prefer the latter over the former?