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Old 01-16-2013, 02:44 AM   #12
bruce01
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Join Date: Mar 2011
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Hi Pablo,

found it on the archives of cram mailing list, the call includes: -L m999 (-L flag is your --lossy-quality-score-spec above). All reads are retained, but you lose column 12+ ('info'). This isn't an issue for me, and the compressed cram file for a 1GB bam is 600MB which is pretty good!
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