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I am running a third-party program that makes use of the htsjdk library.
For some of my samples (BWA alignments) it raises the following exception:
Exception in thread "Thread-5" java.lang.IllegalStateException: Inappropriate call if not paired read
It seems there may be some problem inside the BAM file. However, after running Picard's ValidateSamFile it only finds 1,155 INVALID_MAPPING_QUALITY errors (no errors related to mate reads).
Anyhow, I repaired the bam file using Picard's CleanSam and rerun the third-party program.
The "Inappropriate call if not paired read" error persisted.
How could I solve this, please?
Thanks in advance,