Common problems when running the GATK

This page is a collection of common problems users have encountered while trying to run the GATK.

1. The GATK throws an ERROR that mentions something about an "Invalid file pointer" or a "SAM text reader"

First, please confirm that your BAM file is not malformed. You can use Picard's ValidateSamFile tool.

Next, try deleting the bam index and re-indexing it (with e.g. 'samtools index myfile.bam').