For long chromosomes (800Mb), HaplotypeCaller (GATK4) is used to detect mutations. When it runs to 536Mb, it always encounters HaplotypeCaller-Shutting down engine. the log as follows:
gatk HaplotypeCaller --emit-ref-confidence GVCF -R fa -dont-use-soft-clipped-bases -L chr1A -O out.vcf.gz
How can I solve this problem without splitting the chromosome?
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