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Error stack trace Indexoutofboundsexception

max_shpakmax_shpak Austin TXMember

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
at java.util.ArrayList.rangeCheck(ArrayList.java:635)

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

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