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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

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    Kshama Aswath

    Hi 

    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.

    MY COMMAND:

    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?

    GATK/4.1.8.0

    ERROR:

    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] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 39.91 minutes.

    Runtime.totalMemory()=3758620672

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

            at htsjdk.samtools.util.MergingIterator.next(MergingIterator.java:107)

            at java.util.Iterator.forEachRemaining(Iterator.java:116)

            at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)

            at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)

            at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)

            at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)

            at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)

            at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)

            at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)

            at org.broadinstitute.hellbender.engine.MultiVariantWalker.traverse(MultiVariantWalker.java:118)

            at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1049)

            at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)

            at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)

            at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)

            at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163)

            at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)

            at org.broadinstitute.hellbender.Main.main(Main.java:292)

     

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