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.
Error stack trace Indexoutofboundsexception
I have been trying to run IndelRealigner with the following commands ($tumorPfx etc are file names)
java -d64 -jar $gatkJar -R $hgReference -T IndelRealigner -rf BadCigar -I $tumorPfx.bam -known $G1000_Mills -known $G100\
0_Phase1_Indels -targetIntervals $tumorSample.intervals -o $tumorPfx.realn.bam
and have been getting the following output and error:
ERROR stack trace
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
On this website, I found a similar error with somebody trying to run HaplotypeCaller, albeit with Index and Size = 3, where it was remarked that it may be due to a bug or a java version issue. Is the same thing going on here?
Thank you, Max