Tophat 2.1.1 reports identical alignments, related to a similar issue with HISAT2. The SAM records are identical, and cause troubles with downstream tools. Is there a way to limit these duplicate alignments? Or should we wait until this is fixed
Exception in thread "main" htsjdk.samtools.SAMException: Value was put into PairInfoMap more than once. 96: null:NB501257:32:HWCMVBGXX:1:21209:24100:6206
at htsjdk.samtools.CoordinateSortedPairInfoMap.ensureSequenceLoaded(CoordinateSortedPairInfoMap.java:133)
at htsjdk.samtools.CoordinateSortedPairInfoMap.remove(CoordinateSortedPairInfoMap.java:86)
at picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap.remove(DiskBasedReadEndsForMarkDuplicatesMap.java:61)
at picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:442)
at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:193)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
Tophat 2.1.1 reports identical alignments, related to a similar issue with HISAT2. The SAM records are identical, and cause troubles with downstream tools. Is there a way to limit these duplicate alignments? Or should we wait until this is fixed
Sofware versions: samtools: 1.3.1 Picard 2.2.2 Tophat 2.1.1
Picard Exception:
Locating the offending reads: