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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 for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
GATK - HaplotypeCaller is so slow, is this normal??
I have 15 exome-seq samples, and have been using BWA-PiCard-GATK pipeline to do the variant calling. I did not realize GATK is so slow until I have to analyze this large number of samples. In this HaplotypeCaller step, each sample seems to take at least 2 days (48+ hours). Is this normal is there's something I did wrong? Below is my command, is there anything wrong or GATK-HaplotypeCaller is known this slooooow?
java -Xmx10g -Djava.awt.headless=true -jar
-T HaplotypeCaller \
-minPruning 3 \
-dcov 10 \
-R ./GATK_ref/hg19.fasta \
-I ./GATK/BQSR/sample1_realign.recal.compressed.bam \
Is there anything I did wrong with this command? or anything I can change to make it run faster? I am using GATK 2.5 by the way. thanks!