Question

gatk-funcotator data source

1

Entering edit mode

10 weeks ago

ashaneev07 ▴ 40

Hello all,

I am seeking clarification regarding the data sources provided with the GATK Funcotator tool. The README.txt file does not clearly specify whether the data sources are intended for annotating germline or somatic variants. This ambiguity is impacting our ability to appropriately utilize the data.

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gatk datasource germline funcotator • 342 views

ADD COMMENT • link 10 weeks ago by ashaneev07 ▴ 40

score 2 · Answer 1 · 2024-09-10

From their google cloud repo, the other README.txt file (https://storage.googleapis.com/broad-public-datasets/funcotator/README.txt) says the following:

Data Sources Info
--------------------
Currently all prebuilt data sources are for Homo Sapiens data on either hg19 or
hg38.  The data sources are split into two use cases - Somatic and Germline.

Somatic data sources have a version number ending in 's'.
Germline data sources have a version number ending in 'g'.

Given that the file name for the one you had posted ended in s, I'm guessing that would be a somatic data source. (I can understand the confusing though, given that the use case says somatic and the README section below it says germline)