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Old 06-30-2013, 10:23 PM   #3
sdriscoll
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Location: San Diego, CA, USA

Join Date: Sep 2009
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As far as I know the picard people are working with the bwa people to get the two programs to be more compatible. BWA MEM 0.7.4 should still work. The -M option is going to be gone and instead they are going to use a new flag which will have to be picked up by samtools and picard - but like I said they are all working together on this. I can't explain the seg-fault but I do know that the latest version of MEM has done away with what the -M option used to do. If you back up to a previous version of MEM it should still work. I'm using '0.7.4-r389-beta' and it mostly works. The bwa aln/sampe pipeline is broken in that it fails to properly annotate the 'XA' field of the alignments which triggers a bug in samtools if you attempt to run those alignments through it. However, that version's 'MEM' works perfectly for me (on Mac and Linux).
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/* Shawn Driscoll, Gene Expression Laboratory, Pfaff
Salk Institute for Biological Studies, La Jolla, CA, USA */
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