Question: Does GATK provide datasets to test their pipelines? (Learning purpose)
0
gravatar for yussab
10 weeks ago by
yussab10
Italy
yussab10 wrote:

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

data oncology gatk • 216 views
ADD COMMENTlink modified 10 weeks ago by genomax92k • written 10 weeks ago by yussab10
2

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

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by igor11k

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?

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by genomax92k
2

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.

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by igor11k

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.

ADD REPLYlink written 10 weeks ago by newbio17260

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??

ADD REPLYlink written 10 weeks ago by yussab10
3
gravatar for genomax
10 weeks ago by
genomax92k
United States
genomax92k wrote:

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

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by genomax92k

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

ADD REPLYlink written 10 weeks ago by igor11k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1216 users visited in the last hour