#1 BWA -mem missing XO tag

[Patricia Goerner]

Ran into the following error running Mobster:
Exception in thread "main" java.lang.IllegalStateException: Iteration in progress
at net.sf.samtools.BAMFileReader.query(BAMFileReader.java:347)
at net.sf.samtools.SAMFileReader.query(SAMFileReader.java:363)
at org.umcn.me.pairedend.AnchorClusterer.clusterClippedReads(Unknown Source)
at org.umcn.me.pairedend.AnchorClusterer.clusterSplitAnchorsToBAM(Unknown Source)
at org.umcn.me.pairedend.AnchorClusterer.runFromPropertiesFile(Unknown Source)
at org.umcn.me.pairedend.Mobster.main(Unknown Source)

I ended up noticing that while bwa is an accepter aligner for the input bam files, it seems that bwa -mem is not as there is no XO tags generated. Is there a way to use Mobster on my files aligned with bwa -mem? AKA another tag is could use instead of the XO?

Thanks!

[Jayne Hehir-Kwa]

The latest version of Mobster supports bwaMem and can be found at https://github.com/jyhehir/mobster