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We are working on a custom gtf file with multiple overlapping features for SARS-CoV-2, but viralrecon won't let you use a gtf file as annotation file.
Depending if the input annotation file is a gff or a gtf, SNPEFF_BUILD process should be changed, because now it only works for gff files:
viralrecon/modules/local/snpeff_build.nf
Line 49 in 23e3441
Also, some additional changes are needed in the make_variants_long_table.py to allow overlapping features to appear in the results table.
An example of the original variants_long_table output:
An example of the table we want to obtain:
The text was updated successfully, but these errors were encountered:
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Description of feature
We are working on a custom gtf file with multiple overlapping features for SARS-CoV-2, but viralrecon won't let you use a gtf file as annotation file.
Depending if the input annotation file is a gff or a gtf, SNPEFF_BUILD process should be changed, because now it only works for gff files:
viralrecon/modules/local/snpeff_build.nf
Line 49 in 23e3441
Also, some additional changes are needed in the make_variants_long_table.py to allow overlapping features to appear in the results table.
An example of the original variants_long_table output:
![image](https://private-user-images.githubusercontent.com/25959991/261533043-71aad992-d8bd-4371-8206-e650d46794ac.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.kKX-hJtvYbdpbrlkuFGTj7z8DrRJZKuxcu7mdLgc8Rs)
An example of the table we want to obtain:
![image](https://private-user-images.githubusercontent.com/25959991/261533128-60e817de-48a1-4c0c-a3dd-248a1844274b.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.pi8q80L-zQc8xXWBP9Gkji3GnhjEg_Cx-rx9QzeXZx0)
The text was updated successfully, but these errors were encountered: