Question: Key DP found in VariantContext field FILTER error
0
gravatar for Learner
12 months ago by
Learner 200
Learner 200 wrote:

I am trying to merge 4 samples vcfs that are different from each other before annotation. I am using this technique Merging multiple vcfs with GATK's CombineVariants but I get the following error. I cannot understand what is the issue. I found that here they are mentioning that the header has issue https://gatkforums.broadinstitute.org/gatk/discussion/3962/genotypeandvalidate-error-key-callstatus-found-in-variantcontext-field-info

but I don't know how to fix that

##### ERROR stack trace 
java.lang.IllegalStateException: Key DP found in VariantContext field FILTER at chrM:16185 but this key isn't defined in the VCFHeader.  We require all VCFs to have complete VCF headers by default.
    at htsjdk.variant.vcf.VCFEncoder.fieldIsMissingFromHeaderError(VCFEncoder.java:173)
    at htsjdk.variant.vcf.VCFEncoder.getFilterString(VCFEncoder.java:154)
    at htsjdk.variant.vcf.VCFEncoder.encode(VCFEncoder.java:106)
    at htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:222)
    at org.broadinstitute.gatk.engine.io.storage.VariantContextWriterStorage.add(VariantContextWriterStorage.java:213)
    at org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub.add(VariantContextWriterStub.java:273)
    at org.broadinstitute.gatk.tools.walkers.variantutils.CombineVariants.map(CombineVariants.java:392)
    at org.broadinstitute.gatk.tools.walkers.variantutils.CombineVariants.map(CombineVariants.java:143)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
    at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
    at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
    at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:98)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:323)
    at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
    at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.8-0-ge9d806836):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Key DP found in VariantContext field FILTER at chrM:16185 but this key isn't defined in the VCFHeader.  We require all VCFs to have complete VCF headers by default.
##### ERROR -------------------
genome • 396 views
ADD COMMENTlink modified 12 months ago by Pierre Lindenbaum127k • written 12 months ago by Learner 200
2
gravatar for Pierre Lindenbaum
12 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

It's clearly explained:

Key DP found in VariantContext field FILTER at chrM:16185 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.

your vcf is missing a formal declaration of your FILTER named DP in the vcf header.

##FILTER=<ID=DP,Description="what is that filter">
ADD COMMENTlink written 12 months ago by Pierre Lindenbaum127k

@Pierre Lindenbaum I added that into the header. then it gives error on Key GQ found in VariantContext field FILTER at chrM:16185 but this key isn't defined in the VCFHeader, should I add this too and add as many as they ask? I also get an error like

ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:/Users/admin/Desktop/gatk-3.8-0/GenomeAnalysisTK.jar!/META-INF/log4j-provider.properties
ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console...

do you know if there is something to do with that?

ADD REPLYlink modified 12 months ago • written 12 months ago by Learner 200
1

the message about log4j should be considered as a warning.

ADD REPLYlink written 12 months ago by Pierre Lindenbaum127k
1

then it gives error on Key GQ found in VariantContext field FILTER at chrM:16185

same problem

same solution

ADD REPLYlink written 12 months ago by Pierre Lindenbaum127k
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