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