Remove variants from merged VCF file - CombineVariants

Hi,
I used GATK to merge two VCF files using CombineVariants tool. In the downstream analysis (in Minimac3) I get following error:

Missing Value for Individual : GS000019695-ASM at Marker : 1:47267

Is there an option in CombineVariants or SelectVariants to exclude markers that are missing in one file?

Thank you very much.
Nirmala

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Answers

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭
    edited October 2018

    Hi @Nirmala,

    I'm not familiar with Minmac3. It would be helpful to see what the record at 1:47267 looks like and also for you to explain what you mean by marker. If what you want is to exclude the records in VCF-A from VCF-B, you can use -XL VCF-A in your command. GATK tools will take each position in VCF-A as if an interval and exclude it from analysis. If on the other hand you wish to filter based on genotype, see Tutorial#12350.

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