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FilterMutectCalls did not give any records with 'PASS' in the filter field

jingmengjingmeng AustraliaMember

Hi, I used FilterMutectCalls to filter several VCF files one by one:

java -jar ~/gatk-4.0.5.1/gatk.jar FilterMutectCalls -V original.vcf.gz -O filtered.vcf.gz

And in every output file filtered.vcf.gz, there is no record with 'PASS' in the filter field.

I ran other tools on the same bam files, and they all output variants that passed their corresponding filters.

I use the default parameters when running FilterMutectCalls. It is strange that there are no variants in the filtered.vcf with 'PASS' in the filter field. Can you please help me how to fix it? Thank you!

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Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @jingmeng
    Hi,

    Have a look at this. If you use the latest version, the PASS field should be restored.

    -Sheila

  • jingmengjingmeng AustraliaMember

    Hi, Sheila. I used the version gatk-4.0.5.1 to detect variants. Then I used the latest version gatk-4.0.7.0 to filter VCF file as you advised, but I got an error:

    09:24:35.566 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/jingmeng/Downloads/gatk-4.0.7.0/gatk-package-4.0.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
    09:24:35.665 INFO FilterMutectCalls - ------------------------------------------------------------
    09:24:35.665 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.0.7.0
    09:24:35.665 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
    09:24:35.665 INFO FilterMutectCalls - Executing as [email protected] on Linux v4.15.0-24-generic amd64
    09:24:35.665 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_181-8u181-b13-0ubuntu0.16.04.1-b13
    09:24:35.665 INFO FilterMutectCalls - Start Date/Time: 14 August 2018 9:24:35 AM
    09:24:35.665 INFO FilterMutectCalls - ------------------------------------------------------------
    09:24:35.666 INFO FilterMutectCalls - ------------------------------------------------------------
    09:24:35.666 INFO FilterMutectCalls - HTSJDK Version: 2.16.0
    09:24:35.666 INFO FilterMutectCalls - Picard Version: 2.18.7
    09:24:35.666 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
    09:24:35.666 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
    09:24:35.666 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
    09:24:35.666 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
    09:24:35.666 INFO FilterMutectCalls - Deflater: IntelDeflater
    09:24:35.666 INFO FilterMutectCalls - Inflater: IntelInflater
    09:24:35.666 INFO FilterMutectCalls - GCS max retries/reopens: 20
    09:24:35.666 INFO FilterMutectCalls - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
    09:24:35.666 INFO FilterMutectCalls - Initializing engine
    09:24:35.939 INFO FeatureManager - Using codec VCFCodec to read file file:///media/jingmeng/PhoebeChen/performance/real/mutect/b3.vcf.gz
    09:24:36.068 INFO FilterMutectCalls - Done initializing engine
    09:24:36.106 INFO ProgressMeter - Starting traversal
    09:24:36.107 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
    09:24:36.147 INFO FilterMutectCalls - Shutting down engine
    [14 August 2018 9:24:36 AM] org.broadinstitute.hellbender.tools.walkers.mutect.FilterMutectCalls done. Elapsed time: 0.01 minutes.
    Runtime.totalMemory()=642252800
    java.lang.ArrayIndexOutOfBoundsException: 1
    at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2FilteringEngine.applyBaseQualityFilter(Mutect2FilteringEngine.java:120)
    at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2FilteringEngine.applyFilters(Mutect2FilteringEngine.java:316)
    at org.broadinstitute.hellbender.tools.walkers.mutect.FilterMutectCalls.apply(FilterMutectCalls.java:116)
    at org.broadinstitute.hellbender.engine.VariantWalkerBase.lambda$traverse$0(VariantWalkerBase.java:151)
    at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
    at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
    at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
    at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
    at java.util.Iterator.forEachRemaining(Iterator.java:116)
    at java.util.Spliterators$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.VariantWalkerBase.traverse(VariantWalkerBase.java:149)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
    at org.broadinstitute.hellbender.Main.main(Main.java:289)

    How to fix this problem? Thank you.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @jingmeng
    Hi,

    That is odd the PASS is not explicitly there in the 4.0.5.1 output. It looks like the fix went in for 4.0.4.0. Can you do a quick test and run Mutect2 and FilterMutectCalls on a small snippet of a BAM file and check if 4.0.7.0 gives you PASS variants?

    Thanks,
    Sheila

  • jingmengjingmeng AustraliaMember

    Hi Sheila, I ran Mutect2 and FilterMutectCalls on a Exome bam file with gatk-4.0.7.0, and still did not get any PASS variants.

  • jingmengjingmeng AustraliaMember

    Hi ddzhangzz, have you tried the gatk version 4.0.4.0? And can you please let me know how it goes? Thank you.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @jingmeng
    Hi,

    Hmm. Can you post some example records that have a filter name and some that do not?

    Thanks,
    Sheila

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