Problem with DP following CombineVariants

sagipolanisagipolani Posts: 41Member

Hi team,

I've been having some issues with DP following CombineVariants:

I have two vcf files called by different callers - one by GATK UnifiedGenotyper and the other by samtools mpileup.

When I merge the files using CombineVariants, I notice that the DP per each variant is actually equal to the sum of DP of each of the vcf files.
For example: If for a shared variant in both vcf files the DP=8, then the DP in the union file will be DP=16. Neverhteless, if a given variant is not shared by both files, then the DP in the union file will be equal to the input file.

Is there a way resolve this issue?

Thanks!

Best,

Sagi

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,043Administrator, GATK Dev admin

    Hi Sagi,

    If I understand correctly what is your issue, I believe this is actually the desired behavior. Since the program doesn't know these are calls made on the exact same data, it treats them as showing additional evidence for site calls. Is this an issue for your analysis?

    Geraldine Van der Auwera, PhD

  • sagipolanisagipolani Posts: 41Member

    Hi Geraldine,

    Thank you for your swift reply. Regarding your question - yes, this is an issue for me. I just want the initial DPs.

    Any ideas?

    Thanks!

    Sagi

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,043Administrator, GATK Dev admin

    Hmm. Off the top of my head (no guarantees) I guess you could use the UNIQUIFY genotype merge option so that the separate data get treated as coming from different samples, and use the genotype field DP in your analysis...?

    Geraldine Van der Auwera, PhD

  • sagipolanisagipolani Posts: 41Member

    OK I'll give it a shot. I'll let you know how it goes.

    Thanks Geraldine! Always there when you're needed :)

    I really appreciate it.

    Best,

    Sagi

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,043Administrator, GATK Dev admin

    Happy to help -- I hope it works!

    Geraldine Van der Auwera, PhD

  • sagipolanisagipolani Posts: 41Member

    Hi Geraldine,

    I tried out the UNIQUIFY flag, but sadly it didn't work. Any other ideas maybe?

    Thanks!

    Sagi

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,043Administrator, GATK Dev admin

    Just to check, what command line did you use?

    Geraldine Van der Auwera, PhD

  • sagipolanisagipolani Posts: 41Member

    java -Xmx10g -jar GenomeAnalysisTK.jar \
    -R ref.fasta \
    -T CombineVariants \
    --variant:GATK input1.GATK.vcf \
    --variant:samtools input2.samtools.vcf \
    -o output.vcf \
    -genotypeMergeOptions UNIQUIFY
    --filteredrecordsmergetype KEEP_UNCONDITIONAL

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,043Administrator, GATK Dev admin

    Hmm, can you also post a couple of variant records?

    Geraldine Van der Auwera, PhD

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