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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Mutect2 VCF out Tumor Normal

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5 comments

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    Charitra K

    Hi again, 

    This might be helpful to someone like me :)

    Solution:

    gatk SelectVariant has worked for me to exclude normal_sample_name column as well as normal variants from VCF file. It resulted tumor only column showing tumor variants.

    The commands worked for me is :

    gatk FilterMutectCalls Mutect2_Filtered.vcf.gz -R ref.fa --exclude-filtered true --exclude-sample-name normal_sample_name -O Mutect2_Filtered_PASS.vcf.gz

    What I have learned that :

    1. --exclude-filtered true # keeps PASS variants only

    2. --exclude-sample-name normal_sample_name # Removes normal sample column and variants found in normal sample.

    Do I need any corrections here ?

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    David Benjamin

    Charitra K FilterMutectCalls will mark variants found in the normal with the "germline" filter.  Your SelectVariants command would work if you want them excluded from your VCF entirely, as would something involving "grep -v germline" in a UNIX shell.

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    Charitra K

    Thanks David ! 
    I experienced that 

    SelectVariants --exclude-filtered true removes germline variants and keeps all PASS variants.

    This works for me to get all somatic variants.

     

    Please let me know, if I need corrections here .

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    David Benjamin

    i'm not sure about using --exclude-filtered --exclude-sample-name with FilterMutectCalls.  It might be okay, but it might distort the input.  I would feel much better about using those arguments in SelectVariants after running FilterMutectCalls.

    I should also stress that the output of FilterMutectCalls, in which filtered variants are present and denoted by something other than 'PASS' in the FILTER column, is consistent with the VCF spec.  Downstream tools should be able to handle this, although some unfortunately do not.

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    Charitra K

    Yes David, You are right. 
    It was actually my typo mistake to mention FilterMutectCalls, sory, It is actually SelectVariants. 
    I have updated my previous comment (
    SelectVariants).

    SelectVariants is the one to be used as you sugested.

     

    Thank you !

     

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