<p>Hello everyone,</p>

<p>I would like to download somatic SNP data from the <a href='http://tcga-data.nci.nih.gov'>TCGA</a>. But if I have a look at the data matrix right <a href='https://tcga-data.nci.nih.gov/tcga/dataAccessMatrix.htm?mode=ApplyFilter&amp;showMatrix=true&amp;diseaseType=BRCA&amp;tumorNormal=TN&amp;tumorNormal=T&amp;tumorNormal=NT'>here</a>, there are two color codes "Tumor, matched normal" and "Normal, matched Tumor". I looked up the <a href='https://wiki.nci.nih.gov/display/TCGA/Selecting+Data+Sets#SelectingDataSets-Color-CodingDataSets'>online guide</a> and the <a href='https://wiki.nci.nih.gov/display/TCGA/Getting+Started+with+the+Data+Matrix#GettingStartedwiththeDataMatrix-legend'>Getting Started with the Data Matrix</a> guide.</p>

<p>They explain it like</p>

<ul>
<li>TN (Tumor, matched normal) – Data for a tumor tissue for which matched normal tissue exists.</li>
<li>NT (Normal, matched tumor) – Data for normal tissue for which matched tumor tissue exists.</li>
</ul>

<p>But where is the difference?</p>

<p>May some of you are more experienced using TCGA then me.</p>

<p>With all the best,</p>

<p>Mario</p>

There is no difference between TN and NT for somatic mutations, because tumors and normals are paired up for somatic variant calling. It only makes sense for data generated separately for tumors/normals... like RNA-seq or methylation assays. The data matrix doesn't have a very intuitive interface because they tried to generalize the filtering UI for different data types.

I'd recommend downloading the somatic mutations (MAF files) directly from the [TCGA DCC][1] or from [Firehose][2]. Read more about TCGA MAF files [here][3].

You can also use the [firehose_get][4] script to download latest available MAFs that are fed into Firehose. Here's how to do that:

```
wget http://gdac.broadinstitute.org/runs/code/firehose_get_latest.zip
unzip firehose_get_latest.zip
./firehose_get -b -only Mutation_Packager_Calls data latest
```

To list the other kinds of data (like `Mutation_Packager_Calls` in the command above) look them up [here][5].

 [1]: https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/
 [2]: http://gdac.broadinstitute.org/runs/stddata__latest/samples_report/index.html
 [3]: https://www.biostars.org/p/69222/
 [4]: https://confluence.broadinstitute.org/display/GDAC/Download
 [5]: http://gdac.broadinstitute.org/runs/stddata__latest/data/