Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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 184.108.40.206