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Ensembl / ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
https://www.ensembl.org/vep
Apache License 2.0
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Adding data in ".txt" or "tsv" format to annotations #1581

Closed Alex2006gene closed 10 months ago

Alex2006gene commented 10 months ago

Hello, I want to add data like inheritance pattern from databases like OMIM to my annotations with VEP but they provide us their data in the ".txt" or ".tsv" formmats. How can i convert them to suitable formats or use them in anywhay with VEP? I use vep version 110.1

nakib103 commented 10 months ago

Hello @Alex2006gene,

Thanks for you r query!

A good way to add additional annotation to VEP result is using the --custom option. There are several type of file format supported but you might find bed to be useful for your purpose. The files need to have genomic co-ordinates and be tabix indexed for VEP to calculate variant overlaps. You can find a detailed description in the doc - https://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html

Best regards, Nakib

Alex2006gene commented 10 months ago

Thank you Nakib for your kind response

sounkou-bioinfo commented 9 months ago

Hello @Alex2006gene,

Thanks for you r query!

A good way to add additional annotation to VEP result is using the --custom option. There are several type of file format supported but you might find bed to be useful for your purpose. The files need to have genomic co-ordinates and be tabix indexed for VEP to calculate variant overlaps. You can find a detailed description in the doc - https://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html

Best regards, Nakib Hi @nakib103 , i have a question with regard to the bed annotation output. i used a bed 12 file and output vep in json format, the custom annotation is including only name:chr:start-end. Is there a way to specify which annotations are transfered in the case of a bed file. Thanks in advance

nakib103 commented 9 months ago

Hello @sounkou-bioinfo,

For bed, VEP consider the 4th column as feature identifier and add it as annotation. See more here - https://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html#custom_formats

It will only annotate as "name":{chr:start-end} if it cannot parse the bed file and retrieve the 4th column. Can you check your bed format is correct.

Best regards, Nakib