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tried removing Mutect2 parameters

atariatari SwitzerlandMember

I tried to remove the -tumor and -normal parameter from the Mutect2 command.
It runs and produces as output a vcf file much bigger than the one we obtain including those parameters.
I am sort of curious to know what's the difference in including/excluding those parameters. Thx a lot.

Best Answer

Answers

  • AdelaideRAdelaideR Member admin

    HI @atari -

    I am not sure I understand the question. Could you please provide a little more information?

    1.) Command before changing parameters
    2.) Command after changing parameters
    3.) Version of GATK and if you are running it on the cloud or locally.

    Thanks.

  • atariatari SwitzerlandMember

    Hi,
    I used GATK 4.1.2.0 runned locally on our server.

    Command before:
    ./deploydir6/bin/gatk --java-options "-Xmx8g" Mutect2 \
    -R hg38.fa \
    -I bqsr_markedDuplicates_18852.bam \
    -I bqsr_markedDuplicates_18851.bam \
    -tumor 18852 \
    -normal 18851 \
    --germline-resource af-only-gnomad.hg38.vcf.gz \
    -O somatic_m2_2.vcf.gz \
    -bamout tumor_normal_m2_2.bam

    Command after:
    ./deploydir6/bin/gatk --java-options "-Xmx8g" Mutect2 \
    -R hg38.fa \
    -I bqsr_markedDuplicates_18852.bam \
    -I bqsr_markedDuplicates_18851.bam \
    --germline-resource af-only-gnomad.hg38.vcf.gz \
    -O somatic_m2_2.vcf.gz \
    -bamout tumor_normal_m2_2.bam

    Thx.

  • AdelaideRAdelaideR Member admin

    Okay, let me check with the product development team to see what might be happening.

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