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Picard 2.10.4 has MAJOR CHANGES that impact throughput of pipelines. Default compression is now 1 instead of 5, and Picard now handles compressed data with the Intel Deflator/Inflator instead of JDK.
GATK version 4.beta.2 (i.e. the second beta release) is out. See the GATK4 BETA page for download and details.

# NegativeArraySizeException in GATK 3.0.0 / Java7

Member

I was working with FastaAlternateReferenceMaker today. I wanted to use it on two samples. The first sample worked fine. The second sample came up with an error about a few REF values not conforming (e.g. :A) in the vcf. I wrote a script to correct the errors and remove the : from the vcf file. I tried to run it again, but received memory allocation errors. So, I dealt with that and am now allocating 6g for a 15G VCF and a 188M fasta reference. I got it running (I think) and then started getting the NegativeArraySizeException java error. I saw this had come up as a bug in earlier versions of GATK, but it seemed like it had been resolved...perhaps not? Anyhow, this 'quick little run' has taken up the better part of my day and I would be super greatful for some assistance troubleshooting this problem.

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