Empty final PON vcf file from 7 samples

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Yun Yu

• December 18, 2020 08:44

GATK version 4.1.8.1

I want to call somatic SNVs from 7 pairs of tumour-normal WGSs of dogs. To creat a pon, I run the following commands:

gatk --java-options "-Xmx16G -XX:+UseParallelGC -XX:ParallelGCThreads=4" Mutect2 -R $reference -I $normal_bam -max-mnp-distance 0 -O ${sample}.mutect2.vcf.gz

gatk --java-options "-Xmx16G -XX:+UseParallelGC -XX:ParallelGCThreads=4" CombineGVCFs -R $reference --variant DogWUR115.mutect2.vcf.gz --variant DogWUR116.mutect2.vcf.gz --variant DogWUR117.mutect2.vcf.gz --variant DogWUR118.mutect2.vcf.gz --variant DogWUR119.mutect2.vcf.gz --variant DogWUR120.mutect2.vcf.gz --variant DogWUR91.mutect2.vcf.gz -O 7.glp.normal.vcf.gz

gatk --java-options "-Xmx16G -XX:+UseParallelGC -XX:ParallelGCThreads=4" CreateSomaticPanelOfNormals -R $reference --germline-resource ${known_sites} -V 7.glp.normal.vcf.gz -O final_pon.vcf.gz

But I got an empty final_pon.vcf.gz file, without a single SNP there. Do you have any clue for this problem?

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  Genevieve Brandt (she/her)

  • January 05, 2021 22:23

  Hi Yun Yu, this looks like the same question from your other post. Thanks for reposting so we could get to it after our Out of Office dates! 

  Let me know if this is a different question that needs to get resolved.

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  David Benjamin

  • March 03, 2021 14:00

  Yun Yu Only artifacts (and not germline variants) appearing in more than one sample get into the PON.  With only 7 samples it is very possible that no artifact appears more than once.  Unless you have 100+ samples it is best to use one of the PONs in our public google bucket.

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