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How to add sample name column in Maf output from Funcotator?

First of all, I'd like to thank GATK team for providing brilliant software!
I'm new to exome analysis and GATK. I'm analyzing ~10 tumor exome data using GATK4.1.1.0.
I'd like to know how to add sample name in each raw in MAF file from Funcotator output for downstream (MAFtools) analysis.

So far, I tried:
1.
Generated single vcf file from multiple sample input by running Mutect2 with tumor-only mode(I don't have normal samples).
Funcotator was performed on this vcf file, and the maf output file had "Tumor_Sample_Barcode" field but were filled with "__UNKNOWN__".

2.
With vcf from a single sample, run Funcotator, resultant maf file didn't have "Tumor_Sample_Barcode" field.

I know I can do it by using command line sed one by one, but should I do that?

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    @waterhound

    Can you please post the version of gatk you are using and the exact commands you used for calling variants with mutect2 and funcotator.

  • waterhoundwaterhound Member
    edited April 23
    Thank you, Bhanu. I'm using version4.1.1.0.
    Followings are my command.

    ...

    Mutect2 for one sample.
    ```
    /gatk-4.1.1.0/gatk Mutect2 \
    -R /path/human_g1k_v37_decoy.fasta \
    -tumor sample1 \
    -I sample1_sorted.bam \
    -O sample1_variants.vcf.gz \
    -L /path/Broad.human.exome.b37.interval_list \
    --germline-resource /path/af-only-gnomad.raw.sites.b37.vcf.gz
    ```

    and for Funcotator.
    ```
    /gatk-4.1.1.0/gatk Funcotator \
    --variant sample1_variants.vcf.gz \
    --reference /path/human_g1k_v37_decoy.fasta \
    --ref-version hg19 \
    --data-sources-path /path/funcotator_dataSources.v1.6.20190124s \
    --output sample1_variants.funcotated.maf --output-file-format MAF
    ```

    --------------------------

    For multiple samples, Mutect2
    ```
    /gatk-4.1.1.0/gatk Mutect2 \
    -R /path/human_g1k_v37_decoy.fasta \
    -I sample1_sorted.bam \
    -I sample2_sorted.bam \
    -I sample3_sorted.bam \
    -I sample4_sorted.bam \
    -I sample5_sorted.bam \
    -I sample6_sorted.bam \
    -I sample7_sorted.bam \ for
    -O sample1-7_variants.vcf.gz \
    -L /path/Broad.human.exome.b37.interval_list \
    --germline-resource /path/af-only-gnomad.raw.sites.b37.vcf.gz
    ```

    and Funcotator
    ```
    /gatk-4.1.1.0/gatk Funcotator \
    --variant sample1-7_variants.vcf.gz \
    --reference /path/human_g1k_v37_decoy.fasta \
    --ref-version hg19 \
    --data-sources-path /path/funcotator_dataSources.v1.6.20190124s \
    --output sample1-7_variants.funcotated.maf --output-file-format MAF
    ```
  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    HI @waterhound

    You can specify these as override arguments when calling funcotator. You can do this by adding the following arguments to your call:
    --annotation-default normal_barcode:NORMAL_SAMPLE
    --annotation-default tumor_barcode:TUMOR_SAMPLE

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