Usage of Mutect2

Question

[gprashant17]

Hi,

I have been trying to use the Mutect2 of GATK toolkit, and noticed an example usage:

java -jar GenomeAnalysisTK.jar \
-T MuTect2 \
-R reference.fasta \
-I:tumor tumor.bam \
-I:normal normal.bam \
 [--dbsnp dbSNP.vcf] \
 [--cosmic COSMIC.vcf] \
 [-L targets.interval_list] \
 -o output.vcf

Here, I am assuming that the reference.fasta is the genome sequence in fasta format, and tumor.bam is the file containing details about the mapped reads. I am not sure what is normal.bam. Is it the bam file containing details of the mapped reads of a reference transcriptome with the reference genome?

Answer 1

[MatthewP]

Hello, normal here means normal tissue. People need to compare variants from tumor tissue and normal issue(example: PBMC) to find some variants new(somatic) in tumor tissue.

[gprashant17]

Since I do not have the data for any normal tissue from the same human, is there a way to skip this step?

[MatthewP]

Maybe you should try germline pipeline which use HaplotypeCaller instead of Mutect2 .

[kbullaughey]

Mutect2 now supports tumor only mode in addition to the tumor/normal paired mode. It is also possible to have multiple tumor samples from each individual.