The frontline support team will be unavailable to answer questions on April 15th and 17th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!

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, Moderator admin


    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.