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I like the original Mutect a lot and just downloaded second version of MuTect. I've tried it on my exome BAM files aligned in SE and PE modes. Turns out with PE alignments it takes much-much longer to do SNP call (6 days vs less than a day under the same hardware configuration).
Is that due to the local realignment algorithm? Is that expected?
I do understand that this is beta version, just trying to understand and maybe give some feedback.