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GATK4 with Mutect2, calling somatic SNVs and indels with normal-tumor matched sample
Recently, I am working on test different variants callers with one matched tumor-normal sample. I have successfully run the test program with Strelka, MuTect, GATK3+MuTect2. However, the test with GATK4+Mutect2 is not very successful. I cannot find any mutations with PASS flag in the VCF file. I think that's may because I am doing with wrong commands.
Here is the command line. I copy it from the Mutect2 homepage.
gatk --java-options "-Xmx$MAX_MEM" Mutect2 \ -R $GENOME_REFERENCE \ -I $OUT_DIR/$TUMOR \ -I $OUT_DIR/$NORMAL \ -tumor Illumina_cancer \ -normal Illumina_normal \ --germline-resource $GERMLINE \ --af-of-alleles-not-in-resource 0.0000025 \ --disable-read-filter MateOnSameContigOrNoMappedMateReadFilter \ -L $EXON_REGION \ -O $OUT_DIR/$PREFIX.vcf
- Do I need to add an additional PoN file when running a paired samples?
- Could anyone help me to check if the command above could provide a list of somatic Variants with PASS flag? Actually, I didn't get any variants with PASS flag in my VCF file.
My GATK version is 220.127.116.11