Creating PON

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Paulo Ricardo

• July 01, 2024 11:34

REQUIRED for all errors and issues:
a) GATK version used: v.4.4.0
I'm using your lates docker image, docker pull broadinstitute/gatk:latest

That supposely has the function createsomaticPon, however the output it provided me was this:

##contig=<ID=JH584304.1,length=114452>
##contig=<ID=MU069434.1,length=8412>
##contig=<ID=MU069435.1,length=31129>
##normal_sample=normal
##source=CreateSomaticPanelOfNormals
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO (empty)

Warning: CreateSomaticPanelOfNormals is a BETA tool and is not yet ready for use in production (and mention this error, but why does this tool exist if I can't use it?)

Thank you for your attention, because I need this tools, to create a panel with all my normal samples.

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  Paulo Ricardo

  • July 01, 2024 13:17

  13:03:15.796 INFO  CreateSomaticPanelOfNormals - Initializing engine
  13:03:15.999 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/nfs/lobo/JBARATA-NFS/paulo.mendonca/M>13:03:16.191 INFO  CreateSomaticPanelOfNormals - Done initializing engine
  13:03:16.209 INFO  ProgressMeter - Starting traversal                                                                   13:03:16.209 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
  13:03:21.614 WARN  IntelInflater - Zero Bytes Written : 0
  13:03:21.627 INFO  ProgressMeter -     MU069435.1:28842              0.1                922269       10219047.1
  13:03:21.627 INFO  ProgressMeter - Traversal complete. Processed 922269 total variants in 0.1 minutes.
  13:03:21.639 INFO  CreateSomaticPanelOfNormals - Shutting down engine
  [July 1, 2024 at 1:03:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.CreateSomaticPanelOfNormals done. E>Runtime.totalMemory()=989855744
  Using GATK jar /gatk/gatk-package-4.4.0.0-local.jar
  Running:
      java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_wri ... (It read the variants so why is it empty?)

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  Gökalp Çelik

  • July 04, 2024 11:57

  Hi Paulo Ricardo

  CreateSomaticPanelOfNormals requires large number of normal samples analyzed by mutect2 and combined in a GenomicsDB instance preferably to generate a panel of artifacts that could be found in any sample. You may check the documentation from the link below. Page 10 briefly explains this tool.

  https://github.com/broadinstitute/gatk/blob/master/docs/mutect/mutect.pdf 

  If you are using an inbred species as your variant source you may need this source to filter your variants. 

  Regards. 

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