Heads up:
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.
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.
Notice:
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!
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.
Pipeline Index
Geraldine_VdAuwera
Cambridge, MAMember, Administrator, Broadie admin
This document is under construction. It aims to provide an overview of use cases covered by GATK Best Practices workflows.
| Variant Discovery | Germline | Somatic | Notes |
|---|---|---|---|
| Data pre-processing | Single-sample | Single-sample | Same workflow applies to all |
| Short variants: SNPs and Indels | Single-sample & Joint Calling | Tumor-Normal & Tumor-Only | |
| Copy Number Variants (CNVs) | Multisample | Tumor-Normal & Tumor-Only | |
| Structural Variants (SVs) | In progress | TBD |
| Special use cases | Notes |
|---|---|
| Metagenomic analysis (PathSeq) | |
| Mitochondrial short variants | |
| Liquid blood biopsy |
Post edited by Geraldine_VdAuwera on
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Comments
I have used GATK for SNPcalling since 2016. I think when the last version released the old version did not work. I test both version but I got the same error.
The error copied below:
/var/spool/torque/mom_priv/jobs/4716059.brown-adm.rcac.purdue.edu.SC: line 24: GenomeAnalysisTK: command not found
my pipeline is:
GenomeAnalysisTK -nt 23 -T RealignerTargetCreator -R branch_gene.fasta -I JHIN01_WG_aligned_dedup.bam -o forIndelRealigner_JHIN01.intervals
GenomeAnalysisTK -T IndelRealigner -R branch_gene.fasta -I JHIN01_WG_aligned_dedup.bam -targetIntervals forIndelRealigner_JHIN01.intervals -o sorted_JHIN01_WG_aligned.bam
GenomeAnalysisTK -T HaplotypeCaller -R branch_gene.fasta -I sorted_JHIN01_WG_aligned.bam --emitRefConfidence GVCF -variant_index_type LINEAR -variant_index_parameter 128000 -nct 23 -o variants_JHIN01_WG.g.vcf