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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

Evaluating the quality of a germline short variant callset Follow


  • Avatar
    Kshama Aswath


    I am running evaluate variants and encountered this error:

    Now I would like to point out that I had the same error first pass around and then I had seen another post with the same error (ran until chr14 only) and that person had NOT sorted their vcf file, which is exactly what I had done/not done - not sorted vcf file.So I went back and sorted my input vcf file using picard tool and then fed my sorted file into evaluate variant command as shown below: It ran further more until chrX but then spit out this error below(ERROR).

    One thing to point out is my sorted vcf has only few chromosomes I wanted to look at chr2,3,5,7 and 14. Is that an issue? I dont see how, but worth asking. Also is this a bug as I am running the BETA ?

    Any help would be appreciated.


    gatk VariantEval -R Homo_sapiens_assembly38.fasta -eval fgeno_output_sorted.vcf -O fgeno_variant_eval.tbl -D dbsnp_146.hg38.vcf.gz -no-ev -EV CompOverlap -EV CountVariants -EV IndelSummary -EV MultiallelicSummary -EV TiTvVariantEvaluator

    Why am I getting this error even though my file is sorted?



    22:42:07.179 INFO  ProgressMeter -       chrX:124684150             39.6             147787000        3736018.7

    22:42:17.192 INFO  ProgressMeter -       chrX:146492652             39.7             148520000        3738775.7

    22:42:26.416 INFO  VariantEval - Shutting down engine

    [August 15, 2020 10:42:26 PM EDT] done. Elapsed time: 39.91 minutes.


    java.lang.IllegalStateException: The elements of the input Iterators are not sorted according to the comparator htsjdk.variant.variantcontext.VariantContextComparator


            at java.util.Iterator.forEachRemaining(

            at java.util.Spliterators$IteratorSpliterator.forEachRemaining(







            at org.broadinstitute.hellbender.engine.MultiVariantWalker.traverse(

            at org.broadinstitute.hellbender.engine.GATKTool.doWork(

            at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(

            at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(

            at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(

            at org.broadinstitute.hellbender.Main.runCommandLineProgram(

            at org.broadinstitute.hellbender.Main.mainEntry(

            at org.broadinstitute.hellbender.Main.main(


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  • Avatar
    Eva (Evander)

    Thank you for the great explanation!

    I have one comment and one question. 

    The comments is that the link to the figure "The relationship between variant-level concordance and genotype concordance is illustrated in this figure." is not working. 

    And the a question about: "Another popular method is to evaluate concordance against results obtained from a genotyping chip run on the same samples. [...] This is something we do systematically for all samples in the Broad’s production pipelines." Are there any published workflows for this (by GATK)? 

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