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.
Thank you in advance for reading this. Has anyone else had the following problem when running CollectHSmetrics:
[Tue Apr 12 12:17:52 EDT 2016] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 14.54 minutes.
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -1
The Bait and Target I used was just the header of my BAM file pulled by Samtools view header.
I saw something in the FAQ saying that, "The BAM index format imposes a limit of 512MB for a single reference sequence. If this limit is exceeded, various errors may occur depending on what steps have been taken."
Any explanation on how to address this? Thank you again!