We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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.
Ploidy level in HaplotypeCaller in GATK 4.0
Thanks for the new version of GATK (GATK4.0).
We have a pooling of 48 samples and the organism is diploid, we are using ploidy of 96 (48x2=96). earlier when I am using HaplotypeCaller for variant calling in older versions of GATK, I am getting the error not enough memory to run this program., so was unable to run this with HaplotypeCaller earlier. Now when I tried it with GATK 4.0 version I am not getting this error, but a warn message mentioned below
12:40:23.159 WARN HaplotypeCallerGenotypingEngine - Removed alt alleles where ploidy is 96 and original allele count is 3, whereas after trimming the allele count becomes 2. Alleles kept are:[T*, C]
The command line which we have used is below
java -jar -Xmx64g gatk-package-220.127.116.11-local.jar HaplotypeCaller -R tilling.fa -I C1_S1.sorted.bam -O C1_S1.vcf -stand-call-conf 20.0 -ploidy 96
Can you please help us what does the warn message means, whether the command and the options which I am using are right, or I need to include more options for efficient variant calling.
Thanks in advance.