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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.3 (i.e. the third beta release) is out. See the github release page for download and details.

heterozygous indel bug in GATK 2.4-9

Member

Dear GATK team,

I think I found a bug as shown in the attached screenshot. The highlighted line of the vcf file after using UnifiedGenotyper, VariantRecalibrator, ApplyRecalibration, ReadBackedPhasing, SelectVariants, CombineVariants, and SnpEff (following Best Practices) shows

To be sure, I checked the two samples' bams at the PrintReads stage but do not see such a long indel.
Is this a potentially similar bug to http://gatkforums.broadinstitute.org/discussion/2516/rare-homozygous-indel-bug-in-gatk-2-4-9 ?

Jamie

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