sarek
GATK
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sarek
- Recommendations for software or online resources
- Best somatic variant callers?
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GATK4 automated pipelines in existence?
The sarek pipeline from nf-core might interest you
- Workflow Question
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aws batch keeps the "Desired vCPUs" high long after they should be reduced
The issue is specific to https://github.com/nf-core/sarek and/or it's usage of https://www.nextflow.io/
GATK
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GATK4 automated pipelines in existence?
Are you looking for a germline variant calling pipeline? If so, try https://github.com/lifebit-ai/GATK. If you know Nextflow, you can edit the script. Apparently, it uses Docker so you get the containerization.
What are some alternatives?
galaxy - Data intensive science for everyone.
rnaseq-nf - A proof of concept of RNAseq pipeline
mag - Assembly and binning of metagenomes
rnatoy - A proof of concept RNA-Seq pipeline with Nextflow
configs - Config files used to define parameters specific to compute environments at different Institutions
patterns - A curated collection of Nextflow implementation patterns
eager - A fully reproducible and state-of-the-art ancient DNA analysis pipeline
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
rare-disease-wf - (WIP) best-practices workflow for rare disease
hlatyping - Precision HLA typing from next-generation sequencing data
CancerDB - CancerDB: a computable encyclopedia about cancer.