265. Notice Bug affecting BQSR run with Queue scattergather

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created by Geraldine_VdAuwera

on 2012-09-20

We have discovered a bug that seriously impacts the results of BQSR/ BaseRecalibrator when it is run with the scatter-gather functionality of Queue. To be clear, the bug does NOT affect BaseRecalibrator runs performed "normally", i.e. WITHOUT Queue's scatter-gather.

Consequences/ Solution:

Please be aware that if you have been using BaseRecalibrator scatter-gathered with Queue (GATK versions 2.0 and 2.1), your results may be wrong. You will need to redo the base recalibration of your data WITHOUT scatter-gathering.

This issue will be fixed in the next release (version 2.2). We apologize for any inconvenience this may cause you!

Tags:

bqsr, baserecalibrator, queue, scatter-gather, bug

Updated on 2012-09-20