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.

vcf file generated using HaplotypeCaller does not contain dat lines


I typed the following command for finding snps and indels:
java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R chr21/chr21.fa -I chr21/alignments/human38chr21.sorted.bam -o chr21/humanoutput.raw.snps.indels.vcf

I even got the vcf file but it contains only the header and does not contain the data lines.What maybe wrong?
I hae attached the file containing the stack trace.


  • SheilaSheila Broad InstituteMember, Broadie admin


    It looks like HaplotypeCaller did not find any regions that have variants. I know this from "INFO 10:46:36,131 HaplotypeCaller - Ran local assembly on 0 active regions". Do you know of any sites that should be called variant? Can you post IGV screenshots of those sites?


  • aditya123aditya123 USAMember

    Ya I did the analysis on the same fasta file but using samtools.It shows indels but as I said earlier that it is not showing when gatk is used.I have attached the vcf file generated using samtools for your reference.

  • aditya123aditya123 USAMember

    What maybe the problem?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @aditya123 The depth of coverage in your data is extremely low. The HaplotypeCaller is not designed to process such data. Note that the calls you're getting with samtools have very low quality and are not likely to be very reliable. At such low coverage, you have almost zero power to distinguish real variants from sequencing noise. You should probably reevaluate your experimental design.

Sign In or Register to comment.