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MuTect2 tumor only mode: empty VCFs
I am trying to run Mutect2 in tumor only mode without a matching normal. However, when I did this, MuTect2 produced output VCFs that had a full header, but had no variant calls.
Here is a sample command that I ran to produce variant calls for chromosome 1:
module load gatk/3.5.0; java -Xmx10g -Djava.io.tmpdir=$TMP -jar GenomeAnalysisTK.jar -T MuTect2 -R $REFERENCE_GENOME_FA --dbsnp $DBSNP_VCF --cosmic $COSMIC_VCF -dt NONE --input_file:tumor $TUMOR_BAM --intervals chr1:1-249250621 -o $OUTPUT_VCF
Note: I ran a similar command to this (same input files, etc.) using MuTect v1.1.4 and it produced a complete VCF.
Can you please explain if there is anything I need to change?