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.
What does MuTect output means?
Currently, I am working on identification of somatic mutations on exome data. For this, I am using the combination of GATK + MuTect2 using following code:
java -jar /GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar -T MuTect2 -R /ucsc/ucsc.hg19.fasta --dbsnp /broadinstitute/dbsnp_138.hg19.excluding_sites_after_129.vcf -I:normal GATK_haplotype_unifiedgenotype/output_bowtieoutput.bamaddreplaceread.bam -I:tumor /GATK_haplotype_unifiedgenotype/output_bowtieoutput_bamaddreplaceread.bam -o outputmutect.txt
I am not using
<cosmic.vcf> as this is not cancer data. So my questions are:
- Is this command CORRECT to use for identification of somatic mutations on a noncancerous problem? If the answer is NO, please direct me to the correct paper or discussion.
- How do I interpret the output, especially on filter column -- alt_allele_in_normal;clustered_events, alt_allele_in_normal;clustered_events;t_lod_fstar or alt_allele_in_normal;str_contraction. There are other options as well but I cannot find the appropriate documents to understand what does this mean. Please let me know if there is a better way to identify somatic mutations for a rare disease.
Post edited by Geraldine_VdAuwera on