download Variant allele frequency (VAF)

[Paulin]

Hi,

Could you tell me how could I download patiens data with VAF? I want to download a lof of patients' data together.

Thanks for your help.

Xue

[Tali Mazor]

Hi Xue,

There are a few different places you can download mutation data with VAF included. If you started by running a query, you can download the data in the table on the Mutations tab. If you are looking at an individual patient/sample, you can similarly download the data in the mutations table there. Or, if you want to download all the mutation data for a study, you can do so from the Data Sets page, or by clicking the download icon next to the study name in the header in study view.

-Tali

On Tue, Apr 21, 2020 at 8:24 AM Paulin <xuxu...@gmail.com> wrote:

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[Tali Mazor]

Hi Xue,

Among the files that are downloaded, there is a mutation file. In this file are columns for the reference and alternate read counts for each mutation. You can use these to calculate the variant allele frequency: alt_count / (alt_count + ref_count).

-Tali

On Tue, Apr 21, 2020 at 6:14 PM Paulin <xuxu...@gmail.com> wrote:

Hi Tail,

I want to download all the mutation data for a study, and I do so by clicking the download icon next to the study name in the header in study view. But the zip format files do not involve allel frequency, for example: all_stjude_2016

Thanks

Xue

Tali Mazor <tma...@ds.dfci.harvard.edu> 于2020年4月21日周二 上午8:45写道：