I need a PON vcf

[fi1d18]

Thanks a lot

I am trying to run mutect2 in tumour-only mode for which I need a panel of normal (PON)

I have tried somatic-hg38_1000g_pon.hg38.vcf.vcf which gives

./gatk Mutect2 -R resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta -I /data/Continuum/WES/testAlignmentBROADGenome/results/NG-27280_CLTSS_LTS_001A_lib506241_7636_2_MarkedDup_PicMD.bam -O 3.mt2.vcf -tumor NG-27280_CLTSS_LTS_001A_lib506241_7636_2_MarkedDup_PicMD.targeted_sequencing.sample_name --af-of-alleles-not-in-resource 2.5e-06 --germline-resource af-only-gnomad.hg38.vcf.gz -pon somatic-hg38_1000g_pon.hg38.vcf.vcf

A USER ERROR has occurred: Cannot read file:///data/somatic-hg38_1000g_pon.hg38.vcf.vcf because no suitable codecs found

I know gatk4_mutect2_4136_pon.vcf.gz locates here for which I should register in GDC but because I am a postdoctoral researcher, I can not register

Could you please help me to run mutect2 in tumour-only mode using another publicly available PON?

Thanks for any help

[erdikilic]

If you download the pon file from the GATK's buckets, change .vcf.vcf to .vcf.gz and run it again.

[mcollodetti]

Did it work? I had the same problem and that change didn't do it

[fi1d18]

No did not

Fereshteh Izadi @.?anonymous&ep=bwmEmailSignature> Book time to meet with @.?anonymous&ep=bwmEmailSignature>

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From: mcollodetti @.> Sent: Monday, 4 March 2024 19:51 To: broadinstitute/gatk @.> Cc: Angel Izadi @.>; Author @.> Subject: Re: [broadinstitute/gatk] I need a PON vcf (Issue #8477)

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Did it work? I had the same problem and that change didn't do it

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