FilterMuectCalls program request *vcf.stats file

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Henry

• March 20, 2024 08:12
• Edited

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. 

As a result, it was confirmed that ${chr}.mutect.vcf and ${chr}.mutect.vcf.stat files were created for each chromosome. In the previous GATKv4.0.5.1, a stat file was not generated when Mutect2 was running, and FilterMutectCalls did not require a stat file.

 

I updated the version to GATKv4.5.0.0 and confirmed that a stat file was required, and I tried to proceed with the analysis accordingly. However, as mentioned above, I merged the vcf files generated for each chr, but the stat files were also generated for each chromosome, so I couldn't find a way to combine these stat files and put them in FilterMutectCall.

 

When proceeding with Mutect2 vcf call, shouldn't I use the method of combining the results divided by chromosome? If not, I wonder if there is a way to combine the stat files divided by chromosome into one stat file.

0

• 

  Gökalp Çelik

  • March 20, 2024 08:15

  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. 

  https://gatk.broadinstitute.org/hc/en-us/articles/18965297287067-How-to-setup-and-use-temporary-folder-for-GATK-local-execution 

  I hope this helps. 

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  Henry

  • March 21, 2024 01:58
  • Edited

  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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  Gökalp Çelik

  • March 21, 2024 02:17

  Hi again.

  We have a tool for that.

  gatk MergeMutectStats

   

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