Mutect2 vcf.stats file missing

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4.4 years ago

rugarem • 0

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 • 2.0k views

ADD COMMENT • link updated 4.4 years ago by Ram 45k • written 4.4 years ago by rugarem • 0

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Please give us your exact Mutect2 command.

ADD REPLY • link 4.4 years ago by Ram 45k

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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

ADD REPLY • link updated 4.4 years ago by Ram 45k • written 4.4 years ago by rugarem • 0

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