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!

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.

Open Tumor / Normal pair dataset for benchmarking and training

splaisansplaisan Leuven (Belgium)Member ✭✭

Hi,
I am looking for a real tumor normal pair dataset to apply analysis and compare callers. Do you know of one I can get (bam would be quicker but even fastq is OK as I could map against 38 to be up-to-date).
I only found the Texas open data for which I would need to fill a consent which will be an issue when I use that data in training. I would prefer a fully open dataset and do not like the idea of working with two 1000g samples and pretend one is the tumor of the second (maybe good enough for developing software but I want to look at the data and make sense out of it).
Best
Stephane

Best Answers

  • splaisansplaisan Leuven (Belgium) ✭✭
    Accepted Answer

    Thanks Sheila,
    Actually I needed a full genome size sample as this will be used to evaluate both computing time and global genome metrics.
    I found exome-seq datasets for cancer and normal (SRA045832_cancer-exome) and did with that. Not exactly what i wanted but of reduced size and still showing all genes.
    Thanks for your help

Answers

Sign In or Register to comment.