If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.

Is it safe to call variants per chromosome when using HaplotypeCaller?

je_bje_b Member
edited May 2017 in Ask the GATK team


I'm calling variants in a cohort of samples following the best practices recommendations ( When I get to run HaplotypeCaller, the estimated running time escalates to more than a month per sample, which is excessive. A way arround this is to call variants one chromosome/scaffold at a time using the L flag:

java -jar GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-R reference.fasta \
-I sample_realigned.bam \
-L $chr:1+ ###$chr is being passed to the script using a for loop that loops through all the chromosomes in my file \
--emitRefConfidence GVCF \
--variant_index_type LINEAR \
--variant_index_parameter 128000 \
-o sample$1.g.vcf

...and then concatenate the files per sample using CatVariants. This way I can process each sample in less than a day. Later, I run GenotypeGVCFs on all samples together and get my vcf ready for filtering. My question is: Is it safe to do this? Am I affecting HaplotypeCaller capacity to call variants by separating my dataset in many small subdatasets and then combining them again?


Best Answer


  • pateln13pateln13 Member


    I understand this is an older post and things may have been changed since then but need clarification on above response **"You should never run GenotypeGVCFs with intervals that interrupt the HaplotypeCaller intervals" . **

    I always run haplotype caller without any interval list so that I can have complete gVCF files ( especially when it data is generated at multiple locations and sometime from different capture kit ) and then I perform GenotypeGVCFs with all the samples together with by restricting analysis to interval of interest. Is this incorrect approach ? and will it cause higher False Positive/False Negative ?


  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin


    The GATK support team is currently primarily focusing on resolving questions about GATK tool specific errors or abnormal results from the GATK tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

    Please continue to post your questions because we will be mining them for improvements to documentation, resources, and the tools.

    We cannot guarantee a reply, however we ask other community members to help out if you know the answer.

    For more information:

Sign In or Register to comment.