difference between XENA and Original TCGA pan-cancer MC3 calls

[Xinwei Han]

Dear UCSC Xena staff,

I am interested in MC3 pan-cancer somatic mutation calls. I noticed the Xena MC3 file (https://xenabrowser.net/datapages/?dataset=mc3.v0.2.8.PUBLIC.xena&host=https%3A%2F%2Fpancanatlas.xenahubs.net&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443) only has 9104 samples, while the results provided by the original TCGA pan-cancer paper (raw data (https://gdc.cancer.gov/about-data/publications/mc3-2017) have 10295 samples. E.g., "TCGA-23-1022-01" is present in the original TCGA results, but not in the Xena file. What is the reason for such difference? Did Xena apply any filter on the TCGA MC3 results?  

Many thanks for the great browser and organized datasets!

Best regards,

Xinwei

[Jing Zhu]

Which maf file from  https://gdc.cancer.gov/about-data/publications/mc3-2017 are you referring to?

Jing

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[Jing Zhu]

Yes.  download mc3.v0.2.8.PUBLIC.maf.gz, only kept mutations with filter=PASS

Jing

On Wed, Aug 3, 2022 at 8:00 PM Xinwei Han <hanxi...@gmail.com> wrote:

mc3.v0.2.8.PUBLIC.maf.gz

I noticed Xena file only kept mutations with filter=PASS. I guess those samples without any passed mutatation are removed?

Xinwei

[Xinwei Han]

mc3.v0.2.8.PUBLIC.maf.gz

I noticed Xena file only kept mutations with filter=PASS. I guess those samples without any passed mutatation are removed?

Xinwei

On Wed, Aug 3, 2022 at 3:50 PM Jing Zhu <jz...@soe.ucsc.edu> wrote: