Errors in GATK generated Bam file
I have followed the instructions found here https://www.broadinstitute.org/gatk/guide/article?id=3891 to analyze RNA-seq data. However, when I tried to validate the final bam file using ValidateSamFile tool I get the following errors:
Error Type Count
It looks like the Split'N'Trim step is the cause of these errors since I validate the bam files before and after.
Can anyone tell me why I am getting these errors and how to fix them please?
I appreciate your help,