Question: Creating a PON in GATK
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Hi

I am trying to create a panel of normal in Mutect2 but I am getting error

[fi1d18@cyan01 ~]$ gatk --java-options "-Xmx24G"  Mutect2 -R ./hs37d5.fa -I /scratch/fi1d18/example_results/1631_WTSI-COLO_075_b/mapped_sample/HUMAN_1000Genomes_hs37d5_genomic_WTSI-COLO_075_b.dupmarked.bam -tumor-sample /scratch/fi1d18/example_results/1631_WTSI-COLO_075_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_genomic_WTSI-COLO_075_1pre.dupmarked.bam -O normal1_for_pon.vcf.gz


A USER ERROR has occurred: Bad input: Sample /scratch/fi1d18/example_results/1631_WTSI-COLO_075_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_genomic_WTSI-COLO_075_1pre.dupmarked.bam is not in BAM header: [WTSI-COLO_075_b]

You know how to solve this error?

ADD COMMENTlinkeditmoderate 9 months ago F ♦ 3.4k
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What is your version of GATK ?

Seems like -tumor-sample is not a valid option

ADD REPLYlinkeditmoderate 9 months ago
Bastien Hervé
4.2k
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I guess version GATK/4.0

ADD REPLYlinkeditmoderate 9 months ago
F
♦ 3.4k
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1

Well this is the command line to create PON on GATK4

gatk Mutect2 -R ~/Documents/ref/hg38/Homo_sapiens_assembly38.fasta -I HG00190.bam -tumor HG00190 --disable-read-filter MateOnSameContigOrNoMappedMateReadFilter -L chr17plus.interval_list -O 3_HG00190.vcf.gz

-tumor-sample is not an option there

ADD REPLYlinkeditmoderate 9 months ago
Bastien Hervé
4.2k
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Sorry, what happened if simply I skip creating PON and call somatic variants by ?

[fi1d18@cyan01 ~]$ java -jar /home/local/software/GATK/3.7/source/GenomeAnalysisTK.jar -T MuTect2 -R /temp/hgig/fi1d18/hs37d5.fa -I:tumor /scratch/fi1d18/example_results/1631_WTSI-COLO_075_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_genomic_WTSI-COLO_075_1pre.dupmarked.bam -I:normal /scratch/fi1d18/example_results/1631_WTSI-COLO_075_b/mapped_sample/HUMAN_1000Genomes_hs37d5_genomic_WTSI-COLO_075_b.dupmarked.bam -o out.vcf
ADD REPLYlinkeditmoderate 9 months ago
F
♦ 3.4k
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1

If you have multiples normal samples (meaning healthy tissues) it is good practise to create PON from those normals. The panel of normal will catch technical artifacts to improve your variant calling

You have to run Mutect2 tumor-only mode on every normal sample to create one VCF per normal sample. Then use CreateSomaticPanelOfNormals with the list of VCFs to create your PON

Sure you can skip this step but your results will be less significant with a lot of false positive

ADD REPLYlinkeditmoderate 9 months ago
Bastien Hervé
4.2k

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