I need to run GATK 3.8.1 in a pipeline, but IndelRealigner is segfaulting. I would imagine this is the same issue Picard had/has as reported in https://github.com/broadinstitute/picard/issues/1329 where the Intel deflator segfaults on Mac OSX. In Picard, there is an option to use the JDK inflater instead and bypass this issue. Is there a similar option for IndelRealigner in GATK? 

If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 3.8.1
b) Exact command used: gatk -T IndelRealigner -R chr22.fa -I plasma.sorted.rmdup.addreadgroup.bam -targetIntervals plasma.forIndelRealigner.intervals -o plasma.realignedBam.bam
c) Entire error log:

INFO  15:30:25,501 HelpFormatter - ------------------------------------------------------------------------------------
INFO  15:30:25,503 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-1-0-gf15c1c3ef, Compiled 2018/02/19 05:43:50
INFO  15:30:25,503 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO  15:30:25,503 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO  15:30:25,504 HelpFormatter - [Thu Jun 24 15:30:25 PDT 2021] Executing on Mac OS X 10.15.7 x86_64
INFO  15:30:25,504 HelpFormatter - OpenJDK 64-Bit Server VM 1.8.0_292-b10
INFO  15:30:25,507 HelpFormatter - Program Args: -T IndelRealigner -R chr22.fa -I plasma.sorted.rmdup.addreadgroup.bam -targetIntervals plasma.forIndelRealigner.intervals -o plasma.realignedBam.bam
INFO  15:30:25,518 HelpFormatter - Executing as colinrsmall@Colins-MBP on Mac OS X 10.15.7 x86_64; OpenJDK 64-Bit Server VM 1.8.0_292-b10.
INFO  15:30:25,518 HelpFormatter - Date/Time: 2021/06/24 15:30:25
INFO  15:30:25,518 HelpFormatter - ------------------------------------------------------------------------------------
INFO  15:30:25,518 HelpFormatter - ------------------------------------------------------------------------------------
INFO  15:30:25,569 NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/colinrsmall/Documents/GitHub/cfSNV/tools/GenomeAnalysisTK.jar!/com/intel/gkl/native/libgkl_compression.dylib
INFO  15:30:25,654 GenomeAnalysisEngine - Deflater: IntelDeflater
INFO  15:30:25,654 GenomeAnalysisEngine - Inflater: IntelInflater
INFO  15:30:25,654 GenomeAnalysisEngine - Strictness is SILENT
INFO  15:30:25,727 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO  15:30:25,732 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO  15:30:25,748 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
INFO  15:30:25,821 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO  15:30:25,825 GenomeAnalysisEngine - Done preparing for traversal
INFO  15:30:25,825 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO  15:30:25,825 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
INFO  15:30:25,825 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
INFO  15:30:25,834 ReadShardBalancer$1 - Loading BAM index data
INFO  15:30:25,835 ReadShardBalancer$1 - Done loading BAM index data
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x000000011feab6f7, pid=7088, tid=0x0000000000001603
#
# JRE version: OpenJDK Runtime Environment (8.0_292-b10) (build 1.8.0_292-b10)
# Java VM: OpenJDK 64-Bit Server VM (25.292-b10 mixed mode bsd-amd64 compressed oops)
# Problematic frame:
# C  [libgkl_compression1471945476584797032.dylib+0x76f7]  deflate_medium+0x867
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /Users/colinrsmall/Documents/GitHub/cfSNV/demo/hs_err_pid7088.log
#
# If you would like to submit a bug report, please visit:
#   https://github.com/AdoptOpenJDK/openjdk-support/issues
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#