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thanks for your email. Here is the error message I've been getting when running GenomeSTRiP on 50 genomes (bwa-aligned, GATK indel realigned and quality recalibrated):
So it complains that the insert size of the left and right mate don't agree. It only happens very rarely - on 50 high-coverage whole genomes the error was reported 4 times. Is there a way to prevent GenomeSTRiP from crashing at those instances, e.g. printing a warning instead of an error?
Also, if you have seen this error before, do you happen to know whether the mismatch in insert size might be something that is introduced during GATK realignment?
Thanks a lot!