I have two samples with the following errors. One had an error in Picard MarkDuplicates. The other in GATK IndelRealigner. Both samples were mapped using BWA on paired-end data.
Does anyone know of a way to resolve these errors without removing reads from the sample? Any input at all is greatly appreciated
In Picard:
and in GATK:
Does anyone know of a way to resolve these errors without removing reads from the sample? Any input at all is greatly appreciated
In Picard:
Code:
Exception in thread "main" net.sf.picard.PicardException: Value was put into PairInfoMap more than once. 2: foo:USI-EAS034_4_PE1_FC304CLAAXX:2:22:534:490 at net.sf.picard.sam.CoordinateSortedPairInfoMap.ensureSequenceLoaded(CoordinateSortedPairInfoMap.java:124) at net.sf.picard.sam.CoordinateSortedPairInfoMap.remove(CoordinateSortedPairInfoMap.java:78) at net.sf.picard.sam.DiskReadEndsMap.remove(DiskReadEndsMap.java:61) at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:294) at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:117) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:175) at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:101)
Code:
##### ERROR MESSAGE: Exception when processing alignment for BAM index USI-EAS034_2_PE_FC307TBAAXX:3:79:1633:1917 2/2 45b aligned read.
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