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Mutect2 analysis results in a empty output bam file and a vcf file with only the header

Hello, I write to report a problem I encountered while using Mutect2.

In short, I performed pre-processing on two sets of paired-end fastq files (control and tumor) according to the gatk4 best practices. Then I perform Mutect2 analysis with this command:

gatk --java-options "-Xmx2g" Mutect2 -R /path/ucsc.hg19.fasta -I S3.bam -I S1.bam -tumor tumor -normal ctrl --germline-resource /path/af-only-gnomad.raw.sites.hg19.vcf --af-of-alleles-not-in-resource 0.001 -disable-read-filter MateOnSameContigOrNoMappedMateReadFilter -O 1_somatic_m2.vcf.gz -bamout 2_tumor_normal_m2.bam -L exons.bed

I do not get any errors, the last lines of the st output look like this:

20:53:49.380 INFO ProgressMeter - chrUn_gl000249:36601 361.1 13527466 37460.5
20:53:49.380 INFO ProgressMeter - Traversal complete. Processed 13527466 total regions in 361.1 minutes.
20:53:49.397 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 10.407843391
20:53:49.397 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 951.4249066770001
20:53:49.397 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 3230.28 sec
20:53:49.431 INFO Mutect2 - Shutting down engine
[May 3, 2019 8:53:49 PM CEST] done. Elapsed time: 361.18 minutes.
Tool returned:

However the output bam file and is empty, and the output vcf file contains only the header; what I am doing wrong?

I also tried to run the command without the -L flag.

Thank you in advance.

Best Answer


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