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combing or merging vcf

Dear All,
i need to seek your advice in combining vcf files using combinevariants
i have six samples and i did variant calling separately using unified genotyper.
i need to know can i use this command by specifying --variant six times for each vcf and can get ALL variants in all six files
i dont want unique or common even if they have some common. this -genotypeMergeOptions UNIQUIFY is confusing
java -Xmx2g -jar GenomeAnalysisTK.jar \
-R ref.fasta \
-T CombineVariants \
--variant input1.vcf \
--variant input2.vcf \
-o output.vcf \
-genotypeMergeOptions UNIQUIFY
i want to create mutli-sample vcf file like the one in 1000genomes


  • tommycarstensentommycarstensen ✭✭✭ United KingdomMember ✭✭✭

    @Huma, fellow user here.

    Is it an option for you to do joint calling? You can read about the benefits of joint calling here.

    @h_asif said:
    i need to know can i use this command by specifying --variant six times for each vcf

    Yes, please see the example in the documentation.

    @h_asif said:

    this -genotypeMergeOptions UNIQUIFY is confusing

    The documentation describes the UNIQUIFY argument.

  • h_asifh_asif Member

    thank you for your reply. Actually what i actually want was to merge my 6 six vcf files into one vcf like we do when we generate multi-vcf calling bu unified genotyper. i generated many vcf-subsections that i need from every file from each sample and now want to merge them

  • SheilaSheila admin Broad InstituteMember, Broadie, Moderator admin


    I am not sure I understand your question. The command you originally posted should do what you are asking.


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