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How to combine gVCFs form different chromosomes

analyst123analyst123 Boston, MAMember

I have gVCFS genberated by haplotypecaller (gatk 3.5). 3 sets, 2 of them have same chromosome different samples, 200 each, and one has different chromosomes different samples. What would be the best way to GenotypeGVCFs in my case, would it accept these 3 sets of data.



Best Answer


  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭


    I'm a little confused. Are all the samples from the same species? Do you want to perform analysis on all samples together?


  • analyst123analyst123 Boston, MAMember

    Ok, let me explain a bit more. I have 600 human subjects. I did variant calling (hapolotypeCaller) on a chromosome 1 (400 subjects) and generated gVCFs. from these, i run combine GVCF on batches of 200 to generate 2 GVCFs.
    I did variant calling on another 200 on chromosome 2, and generated 1 combined GVCF.
    Now I have 3 GVCFs, i want to generate a single VCF for further analysis, will GenotypeGVCF be able to handle of I need any pre-processing.

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