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GATK variantsToTable output ordering of tumor and normal columns

Hi,

I am using VariantsToTable to populate the vcf to a table.
the vcf file was generated by:

samtools mpileup -Q 20 -q 10 --skip-indels -f Homo_sapiens_assembly19.fasta -l ${merged_mutations} -v -t DP,AD,ADF,ADR,SP -o "${oprefix}".vcf.gz ${Normal_bam} ${Tumor_bam}

I feed normal_bam then tumor_bam.

java -jar /scratch/genomic_med/apps/gatk/default/GenomeAnalysisTK.jar \
-R /scratch/rists/hpcapps/reference/human/broad_hg19/fastas/Homo_sapiens_assembly19.fasta \
-T VariantsToTable \
-V "${oprefix}".vcf.gz \
--allowMissingData \
--showFiltered \
-F CHROM -F POS -F REF -F ALT -F QUAL -F DP -GF PL -GF DP -GF SP -GF AD -GF ADF -GF ADR \
-o "${oprefix}".table

What I found strange is that, sometimes, the output table put tumor_bam associated values before the normal_bam associated values, and sometimes put them after the normal_bam. How does VariantsToTable determine the ordering?

Thanks!
Ming

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Best Answer

Answers

  • SheilaSheila Broad InstituteMember, Broadie admin

    @crazyhottommy
    Hi Ming,

    Are you saying in the output table from VariantsToTable, the values sometimes are switched for the tumor and normal?

    Can you please post an example where the values are reversed in the table and also the corresponding VCF records?

    Thanks,
    Sheila

  • Hi Sheila,

    please find the attachment for a sample vcf file. (I changed the suffix to txt, otherwise can not be uploaded)

    The VariantsToTable output tumor first and then normal.

    CHROM POS REF ALT QUAL DP WGC046561D-combined.PL WGC046561D-combined.DP WGC046561D-combined.SP WGC046561D-combined.AD WGC046561D-combined.ADF WGC046561D-combined.ADR WGC067395D-normal.PL WGC067395D-normal.DP WGC067395D-normal.SP WGC067395D-normal.AD WGC067395D-normal.ADF WGC067395D-normal.ADR
    1 48192 T C,<> 0.0 85 0,41,198,99,210,221 37 2 33,4,0 18,3,0 15,1,0 0,129,191,129,191,191 43 0 43,0,0 27,0,0 16,0,0
    1 59415 T C,<
    > 0.0 55 62,0,117,108,135,195 21 15 15,6,0 2,4,0 13,2,0 0,93,242,93,242,242 31 0 31,0,0 16,0,0 15,0,0
    1 80107 T <> 0.0 68 0,84,220 28 0 28,0 14,0 14,0 0,99,255 33 0 33,0 12,0 21,0
    1 119006 A <
    > 0.0 116 0,160,216 53 0 53,0 22,0 31,0 0,166,176 55 0 55,0 31,0 24,0

    Thank you!
    Ming

    test.txt 236.6K
  • @Sheila said:
    @crazyhottommy
    Hi Ming,

    Are you saying in the output table from VariantsToTable, the values sometimes are switched for the tumor and normal?

    Can you please post an example where the values are reversed in the table and also the corresponding VCF records?

    Thanks,
    Sheila

    Hi Sheila,

    please find the attachment for a sample vcf file. (I changed the suffix to txt, otherwise can not be uploaded)

    The VariantsToTable output tumor first and then normal.

    CHROM POS REF ALT QUAL DP WGC046561D-combined.PL WGC046561D-combined.DP WGC046561D-combined.SP WGC046561D-combined.AD WGC046561D-combined.ADF WGC046561D-combined.ADR WGC067395D-normal.PL WGC067395D-normal.DP WGC067395D-normal.SP WGC067395D-normal.AD WGC067395D-normal.ADF WGC067395D-normal.ADR
    1 48192 T C,<> 0.0 85 0,41,198,99,210,221 37 2 33,4,0 18,3,0 15,1,0 0,129,191,129,191,191 43 0 43,0,0 27,0,0 16,0,0
    1 59415 T C,<> 0.0 55 62,0,117,108,135,195 21 15 15,6,0 2,4,0 13,2,0 0,93,242,93,242,242 31 0 31,0,0 16,0,0 15,0,0
    1 80107 T <> 0.0 68 0,84,220 28 0 28,0 14,0 14,0 0,99,255 33 0 33,0 12,0 21,0
    1 119006 A <> 0.0 116 0,160,216 53 0 53,0 22,0 31,0 0,166,176 55 0 55,0 31,0 24,0

    Thank you!
    Ming

  • SheilaSheila Broad InstituteMember, Broadie admin

    @crazyhottommy
    Hi Ming,

    Ah, I think VariantsToTable outputs the samples based on alphabetical order. Unfortunately, this is not something that will be prioritized/fixed. You can try changing the tumor name to reflect tumor so it is alphabetically after normal.

    -Sheila

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Sure, we'll document this in the tool doc.

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