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 October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.
Genotypegvcfs 3 Week Estimated Run Time for WGS
I am currently running Genotypegvcfs on 86 human WGS using GATK 3.7 and I am experiencing an estimated run time of 3+ weeks. My code is:
java -Xmx120G -Djava.io.tmpdir=/mnt/data_schen/travis/WGS-86/tmp -jar /mnt/data2/travis/bin/gatk_3.7\GenomeAnalysisTK.jar \
-T GenotypeGVCFs \
-R /mnt/data2/travis/REFERENCE/human_g1k_v37_decoy.fasta \
--variant WGS_86.list \
I am using GATK 3.7 to keep my pipeline consistent as I plan on combining these 86 with another 101 WGS samples that were run last year. HTC was used to generate gvcfs for each of the 86 individuals.
When run in multi-thread mode the application crashed with the "Code exception" error. This is very unfortunate as it had an estimated run time of 6 days.
I have read that you suggest running Genotypegvcfs in parallel by separating gvcfs based on chromosome. Do I need to:
- Separate every gvcf of every sample into 22 chromosomes + sex chromosomes (i.e. 187x24) with SelectVariants
- Combine the chromosomes using Combinegvcfs
- Run each chromosome separately through Genotypegvcfs
- Then combine the chromosomes using CatVariants
I am uncertain I fully understand the current recommendations and am looking for advice before moving forward. Are there any alternative methods I may consider?