Key DP found in VariantContext field FILTER error
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2.8 years ago
Learner ▴ 250

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.getFilterString(VCFEncoder.java:154)
at htsjdk.variant.vcf.VCFEncoder.encode(VCFEncoder.java:106)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
##### 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
##### 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 • 1.7k views
2
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2.8 years ago

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.

##FILTER=<ID=DP,Description="what is that filter">

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@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?

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the message about log4j should be considered as a warning.

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

same problem

same solution