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Mutect2 vcf.stats file missing

Hi everyone,

Just wanted to ask if anyone can help me locate the .vcf.stats file supposedly made by Mutect2 along with the .vcf.

I've called my variants using Mutect2 on a cluster, got the vcf but no vcf.stats file. I need that file to filter using FilterMutectCalls. I've tried: find /users/username/ -name "*.vcf.stats" and nothing. The information on the GATK webpage on this issue is no help at all.

I can't seem to specify where the vcf.stats file is dumped by Mutect2 either.

Anyone else run into this problem calling variants on a cluster and resolved it? Much appreciated in advance!

R

gatk mutect2 vcf.stats
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updated by Ram Ram • written by rugarem • rugarem

Please give us your exact Mutect2 command.

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written by Ram Ram

The Mutect2 command as requested below!

/apps/bio/gatk/4.1.4.1/gatk Mutect2 \
-R /ph-users/rugare/cancer_data/samtools_index/Homo_sapiens_assembly38.fasta \
-I /ph-users/rugare/cancer_data/tissue/SRR3401405/outfiles/SRR3401405.bam \
-O /ph-users/rugare/cancer_data/tissue/SRR3401405/outfiles/SRR3401405.vcf
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updated by Ram Ram • written by rugarem • rugarem

Your output directory is under /ph-users/. Why are you looking for the stats file under /users/?

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written by Ram Ram

Hello rugarem

Why did you delete this post?

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written by Ram Ram

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