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.
Using the GATK Unified on a pooling sample
I've got a pool of 80 individuals sequencing data.
Each individual doesn't have index, so that i have just one fastq file and bam file that i cannot sort any sample data from it.
I try to use GATK UnifiedGenotyper v3.3 including "-ploid" option
There're some questions.
- command :
java -Xmx100g -jar /ruby/Tools/GATK/GenomeAnalysisTK-3.3/GenomeAnalysisTK.jar -T UnifiedGenotyper -R ./Ref.fasta -I 1.bam -o 1_unified.vcf --sample_ploidy 160 -minIndelFrac 0.05 --genotype_likelihoods_model BOTH -pnrm EXACT_GENERAL_PLOIDY -nct 4 -nt 10
--sample_ploidy = 160 = 80 (pooling 80 individuals) * ploid ( diploid, 2 )
bamfile size = 3.4GB
SERVER SPEC :
CPU core = 40x
memory = 256G
I've started the process 4 days ago.
The progress percent is 0.3%, and remain time is 176.9 weeks.
I think it's too slow to complete.
I just wonder how long takes time to process GATK UnifiedGenotyper on that data.
Is there any recommendations to improve this job?