To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

How to combine gVCFs form different chromosomes

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, Moderator


    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.

Sign In or Register to comment.