<p>I'm building a somatic variant calling pipeline with <code>snakemake</code>. The pipeline is hosted on Github, and I'd like to use Travis CI for continuous integration testing. Due to privacy concerns, I am looking for a publicly available tumor-normal dataset similar to Genome in a Bottle's NA12878 dataset that I can place online without privacy concerns and use for integration testing. Any sources to find tumor-normal FASTQ data that is publicly available?</p>

CC BY-SA 4.0
2020-01-09T20:53:38.567Z
Are you after whole exome sequencing (WES) or whole genome sequencing (WGS) for you variant calling pipeline?
Kohl Kinning
CC BY-SA 4.0
2020-01-09T23:17:13.657Z
Right now the pipeline only supports WES data, but I'm planning to add WGS support so both data types are of interest!
Tomas Bencomo
CC BY-SA 4.0
2020-01-10T11:44:16.997Z
If the site from the suggested duplicate above doesn't work, do try emailing the study's authors. I did so last year and they were incredibly helpful and actually put the site back up for me! If that isn't possible, leave me a comment here (use `@terdon`) and I can try and get the data to you.
terdon
<variant-calling><snakemake><gatk><public-dataset>
NA12878 equivalent for somatic variant calling
# NA12878 equivalent for somatic variant calling

(Asked by: username_0 on 2020-01-09)

I'm building a somatic variant calling pipeline with `snakemake`. The pipeline is hosted on Github, and I'd like to use Travis CI for continuous integration testing. Due to privacy concerns, I am looking for a publicly available tumor-normal dataset similar to Genome in a Bottle's NA12878 dataset that I can place online without privacy concerns and use for integration testing. Any sources to find tumor-normal FASTQ data that is publicly available?

**Tags:** variant-calling, snakemake, gatk, public-dataset
> **Comments:**
> **username_1**: Are you after whole exome sequencing (WES) or whole genome sequencing (WGS) for you variant calling pipeline?  
> **username_0**: Right now the pipeline only supports WES data, but I'm planning to add WGS support so both data types are of interest!  
> **username_2**: If the site from the suggested duplicate above doesn't work, do try emailing the study's authors. I did so last year and they were incredibly helpful and actually put the site back up for me! If that isn't possible, leave me a comment here (use `@terdon`) and I can try and get the data to you.  

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## 0 answers

