FilterMuectCalls program request *vcf.stats file
REQUIRED for all errors and issues:
a) GATK version used: GATK v4.5.0.0
b) Exact command used:
$java -XX:ParallelGCThreads=12 -Xmx80g -jar $gatk FilterMutectCalls -R ${reference} -V ${pairname}.vcf -O ${pairname}_Filtered.vcf
c) Entire program log:
~/Program/Java/jdk-17.0.5/bin/java -XX:ParallelGCThreads=12 -Xmx80g -jar ~/gatk-package-4.5.0.0-local.jar FilterMutectCalls -R ~/Reference/hg19/Sequence/genome.fa -V HC0263-0014_HC0263-0017.vcf -O HC0263-0014_HC0263-0017_Filtered.vcf
12:41:53.190 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:~/Program/GATK/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
12:41:53.317 INFO FilterMutectCalls - ------------------------------------------------------------
12:41:53.319 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
12:41:53.320 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
12:41:53.320 INFO FilterMutectCalls - Executing as u1200538@cm462 on Linux v3.10.0-1160.25.1.el7.x86_64 amd64
12:41:53.320 INFO FilterMutectCalls - Java runtime: Java HotSpot(TM) 64-Bit Server VM v17.0.5+9-LTS-191
12:41:53.320 INFO FilterMutectCalls - Start Date/Time: March 20, 2024 at 12:41:53 PM KST
12:41:53.320 INFO FilterMutectCalls - ------------------------------------------------------------
12:41:53.320 INFO FilterMutectCalls - ------------------------------------------------------------
12:41:53.321 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
12:41:53.321 INFO FilterMutectCalls - Picard Version: 3.1.1
12:41:53.321 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
12:41:53.321 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
12:41:53.321 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:41:53.321 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:41:53.322 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:41:53.322 INFO FilterMutectCalls - Deflater: IntelDeflater
12:41:53.322 INFO FilterMutectCalls - Inflater: IntelInflater
12:41:53.322 INFO FilterMutectCalls - GCS max retries/reopens: 20
12:41:53.322 INFO FilterMutectCalls - Requester pays: disabled
12:41:53.322 INFO FilterMutectCalls - Initializing engine
12:41:53.427 INFO FeatureManager - Using codec VCFCodec to read file file://~/Somatic_Analysis/HC0263-0014_HC0263-0017/Somatic_SNV_InDel/HC0263-0014_HC0263-0017.vcf
12:41:53.447 INFO FilterMutectCalls - Done initializing engine
12:41:53.619 INFO FilterMutectCalls - Shutting down engine
[March 20, 2024 at 12:41:53 PM KST] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=335544320
***********************************************************************
A USER ERROR has occurred: Mutect stats table HC0263-0014_HC0263-0017.vcf.stats not found. When Mutect2 outputs a file calls.vcf it also creates a calls.vcf.stats file. Perhaps this file was not moved along with the vcf, or perhaps it was not delocalized from a virtual machine while running in the cloud.
I wonder how to make Mutect.vcf.stats file in my case.
Before the running FilterMutectCalls, I completed the Mutect2 Somatic variant call by chromosome. If we use vcf, which is not divided by chromosome, it takes too long, so we divided it by chromosome and proceeded with mutect2 vcf call.
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Hi Henry
This is a known issue of not receiving the stat file when temporary folder unreachable at the end of the GATK run due to workflow managers and cluster access rights. The only solution is to move the temporary directory for Mutect2 to a location that you have proper read write access. You may refer to the document in the link below.
I hope this helps.
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Hello, Gökalp Çelik !
Thank you for your rapidly reply,
I read your adivce, but my issue does not matches your solution.
I got a *vcf.stats file. I want to know if we generate Mutect vcf and vcf.stats file by chromosome, how to make or calculate merged stats file for assigning "FilterMutectCall" process?
I'd appreciate it if you could check it out.
thank you,
[ my workflow ]
1. Mutect2 running by spliiting chr (generated {chr}.vcf and {chr}.vcf.stats)
2. Merged {chr}.vcf to whole.vcf ( ex., merged chr1.vcf, chr2.vcf ... chrY.vcf => whole.vcf )
3. FilterMutectCall ( I made a whole.vcf, but this process request a whole.vcf.stats. *I want to know how to make a whole.vcf.stats file)
I'd appreciate it if you could check it out.
Thank you,
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Hi again.
We have a tool for that.
gatk MergeMutectStats
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