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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

core dumped when using IndexFeatureFinder to generate index for dbSNP.vcf file



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    Gökalp Çelik

    Hi Daniel Rodden

    The core dump message does not seem to be related to the vcf lines but about the executor's script's line number 12 which is the gatk command. If it is a core dump this could also have a java err file somewhere around the execution folder. If not we recommend you to activate verbose gatk error messages using the option below.

    --java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true'

    Increasing the java heapsize using --java-options "-Xmx" option could solve the problem if it is a heapsize issue, however sometimes this could also be due to temporary folder assignment. Can you also try changing the temporary folder to another location where you have plenty of read and write access?

    --tmp-dir /path/to/tmp

    If none of them works you may use tabix on bgzipped vcf files to index

    tabix -p vcf vcffile.vcf.gz

    or you may try using bcftools index option. 

    I hope any of these will help. 

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    Daniel Rodden


    Thanks for your reply. I'm going to try generating the index using tabix and tell you if that works. I'll also try your above suggestions, and report back on what works. Thanks! 

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