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sampleTypes
Q: What TCGA sample types are Firehose pipelines executed upon?

A:  Since inception Firehose analyses have been executed upon tumor samples and then correlated with clinical data.   Nearly all analyses utilize primary solid tumor samples (numeric code 01, short letter code "TP" as given in the TCGA sample type codes table), with two exceptions:

  1. melanoma (SKCM), where we analyze metastatic tumor samples (numeric code 06, short letter code "TM")
  2. acute myeloid leukemia (LAML), which we analyze using primary blood-derived samples (numeric code 03, short letter code "TB")
Also note that each stddata run dashboard contains a samples summary report, which explains why – even though our GDAC mirrors ALL data from the DCC on a daily basis – not every sample is ingested into Firehose*.
*Specifically, we filter out ALL samples listed as Redacted in the TCGA Annotations Manager, and FFPE samples are only available in standard data archives, not analyses.

Programmatically, the FireBrowse patients api will give you a list of all patients in each cohort, either in bulk (all cohorts) or any subset you chose. It doesn’t give the complete aliquot barcode yet, but will in the very near future.  In addition to playing with this API interactively through the FireBrowse UI, there are also  Python, Unix, and R bindings, and even a pip-installable package.

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