If you happen to see a question you know the answer to, please do chime in and help your fellow community members. 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.

GATK HaplotypeCaller isn't calling variants?

Hi guys,

I am working with three genomes from the same species. I have managed to call variants between the reference and two of the genomes but the third seems to be having an issue that I don't know. I processed them exactly in the same pipeline prior to calling the variants on them using HaplotypeCaller. However, on the third genome the algorithm produces an empty vcf file as if it encountered an exact replica of the reference genome. It doesn't seem like its encountering any type of error as the log file shows that it is walking through the genome fine and the standard error file is empty (no error messages)

My code for calling the variants is as follows:

java -Xmx6g -jar Documents/GenomeAnalysisTK-2.6-5-gba531bd/GenomeAnalysisTK.jar -T HaplotypeCaller -nct 4 -R equcab2.fa -I Documents/PhD_work/recal.bam -stand_call_conf 20 -stand_emit_conf 10.0 -o output.raw.snps.indels.vcf 1>> gatk_HaplotypeCaller.log 2>> gatk_HaplotypeCaller.stderr

I would really appreciate if someone can help me out with this.

Thank you! :-)

Best Answer


  • modi2020modi2020 Member

    Thank you so much Geraldine....I realigned it and it worked...yaay!

Sign In or Register to comment.