Fixed a bug with MarkDuplicates in extract.sh.
Fixed a bug with MarkDuplicates in extract.sh.

benranco/SNPpipeline,benranco/SNPpipeline,benranco/SNPpipeline,benranco/SNPpipeline,benranco/SNPpipeline,benranco/SNPpipeline,benranco/SNPpipeline,benranco/SNPpipeline,benranco/SNPpipeline