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Old 11-13-2018, 10:23 PM   #6
Gopo
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Location: Louisiana

Join Date: Nov 2013
Posts: 38
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Sorry, I don't know of a solution. The best I can suggest is to report this to the issues page on the Picard github repo.
https://github.com/broadinstitute/picard/issues

Again, maybe a newer version of Picard or the newest version of samtools (samtools merge) or perhaps sambama (sambamba merge) might work?

Another possibility is to do the merge with CREATE_INDEX=FALSE. Then see if samtools index or sambamba index can make the index of the merged BAM.

Last edited by Gopo; 11-13-2018 at 10:26 PM. Reason: clarity
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