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Can I use UnifiedGenotyper to call somatic variants in tumor/control tissues?

I067569I067569 Member
edited March 2013 in Ask the GATK team


I am interested in the following scenario:
1. sequence tumor and control samples to separate fastq files.
2. Execute read alignment for the 2 samples separately.
3. Execute UnifiedGenotyper with the 2 BAM files (control and tumor) with the following command:

java -jar GenomeAnalysisTK.jar \
-T UnifiedGenotyper \
-R ReferenceGenome.fasta \
-I contro.bam -I tumor.bam \
-D /usr/sap/GenomicsPlatform/dbSNP/dbsnp_137.b37.vcf \
-o output.vcf

Is this a proper usage for UnifiedGenotyper?
How does UnifiedGenotyper refer to the 2 BAM files it recieves as input?
What do I expect to see in the output.vcf file? are they somatic variants which describe the variation between control and tumor samples?

Thank you,

Best Answer


  • Hello Geraldine,

    How does the SomaticIndelDetector fits to overall picture? According to the document ( it can be used to detect indels in tumor-normal paired sample. Is it related to the workaround you mentioned above?


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Amit,

    MuTect is designed to detect somatic SNPs while the SomaticIndelDetector is for somatic Indels. Please note that the SomaticIndelDetector is no longer included in GATK since version 2.4; that tool is now in the hands of a different group here at the Broad Institute. Specifically, the Cancer Group, who also produce MuTect. You can contact them to ask how you can obtain their tools for cancer-related analysis.

  • Hi,
    I was planning to get the somatic mutations by processing the normal and tumor samples separately then with a script filter out the mutations that are found in the normal sample.

    Do you think, that works ?


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Suleyman,

    Please see my previous answer (top of the answers list, in green box).

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