Does GATK provide datasets to test their pipelines? (Learning purpose)

Question

[yussab]

Hi Everyone,

I am working in the oncology field and I would like to test this pipeline .

GATK -Germline short variant discovery (SNPs + Indels)

https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels-

Unfortunately I'm not able to find raw fastq data to test the pipeline.

Does GATK provide datasets to test their pipelines?

I found this article, but unfortunately I'm not able to download the data from the linked source. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4243306/pdf/nihms531590.pdf

Thank you very much, I'm open to every advice about how to handle it. AY

[igor]

You can also check their workshops which have a lot of info and examples: https://drive.google.com/drive/folders/1y7q0gJ-ohNDhKG85UTRTwW1Jkq4HJ5M3?usp=sharing

[GenoMax]

igor : Those workshops appear to be a year+ old going by date stamps. Do you know if they cover all the changes that have happened recently?

[igor]

Some of them are from 2020 (use the directory name, not the modified date to gauge the age). I assume various events stopped in March due to the pandemic. GATK4 has been out for over 2 years and most of the tools have not changed much.

[newbio17]

If it's a simple testing to see how easy the setup is and etc., you can try to look for .fastq files that are publicly available from SRA.

[yussab]

I'm trying this way but I found extremely difficult to find raw data for matched tumor-normal samples. Do you have any advice to search the SRA from NCBI??

Answer 1

[GenoMax]

GATK does provide test data via Google cloud and Amazon AWS.

[igor]

Why do they include RNA-seq Cell Ranger data? That does not seem GATK-related.