Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Exception "Inappropriate call if not paired read"
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,