To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

Does it matter if the intervals of interest file is lexicographicaly sorted or not?

Meaning does it matter if my intervals file goes chr1, chr10, instead of chr1, chr2 ? Additionally, will a command line error occur if bam files are not sorted in coordinate order with respect to the reference?
Thank you


Best Answer


Sign In or Register to comment.