What is exact meaning of filtering in vcf

yhkimyhkim Member
edited November 2017 in Ask the GATK team

Hi, I have question about output vcf using mutect2.

I run the mutect2 using only tumor set,

I got this filtering result like this,

_**clustered_events;homologous_mapping_event;panel_of_normals
clustered_events;homologous_mapping_event;t_lod_fstar
panel_of_normals
clustered_events;panel_of_normals
clustered_events;homologous_mapping_event;panel_of_normals;str_contraction
panel_of_normals;str_contraction

**_
but, the meaning of this describes in vcf,

clustered_events : clustered events (>2) observed in the tumor
panel of normals : Seen in at least 2 samples in the panel of normals

  1. but, I confirmed the variant AF of panel of normals in EXAC database,
    many variant in panel of normals don't have EXAC AF.
    the description of panel of normal said "Seen" in at least 2 samples in normal,
    so, Where was the variant detected in what normal database ??

  2. after reading description of filtering, I thinks, clustered events means "tumor" and panel of normals means "normal".
    but, the result in upper, the meaning of tumor and normal is in together(clustered_events;panel_of_normals ), I don't understand.
    if i want to get real tumor variants, should i remove this filtering ?
    but, most of variant is both meaning.

please answered this question.

thanks.

yh

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @yhkim
    Hi yh,

    Can you post the exact command you ran? If you are using GATK3, can you try with the latest GATK4?

    Thanks,
    Sheila

  • @Sheila

    I used GATK 3.6. this is the command line i uesed,

    java -Xmx4G -jar ${GATK} \
    -T MuTect2 \
    -R ${RefFasta} \
    -I:tumor ${PreProcesseDBam} \
    --dbsnp ${DBSNP} \
    --cosmic ${COSMIC} \
    --normal_panel ${ExAC} \
    -L ${interval_region} \
    -ip 100 \
    --disable_auto_index_creation_and_locking_when_reading_rods \
    -o ${sampleName}.raw.vcf \
    -bamout ${sampleName}.Mutect2.bamout.bam

    is there wrong in command line?

    I will try to used GATK4.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @yhkim
    Hi yh,

    Nothing wrong with your command :smiley:
    However, this may just be an issue in GATK3 MuTect2, and it will not be fixed because GATK4 Mutect2 is about to be released. Let us know if the GATK4 results look good.

    Thanks,
    Sheila

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