No linked file for gene list

KCCG / ClinSV

Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data

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No linked file for gene list #33

Closed melnel000 closed 2 years ago

melnel000 commented 2 years ago

To mark variants affecting user defined candidate genes, a gene list list has to be placed into the project folder and named "testGene.ids". Gene names have to be as in ENSEMBL GRCh37.

There is no linked file for [gene list]

What is the format of this file? Should dI be using gene symbols or ENSEMBL IDs?

Thanks, Melissa

J-Bradlee commented 2 years ago

As far as I know, the current gene list being used by ClinSV can be found for ref-b37 under annotations (at this path refdata-b37/annotation/Homo_sapiens.GRCh37.75.ids) . It is using gene symbols, running the command head refdata-b37/annotation/Homo_sapiens.GRCh37.75.ids gives me the following output:

5S_rRNA
7SK
A1BG
A1BG-AS1
A1CF
A2M
A2M-AS1
A2ML1
A2ML1-AS1
A2ML1-AS2

Also your link provided is broken.

Hope this helps.