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I am recently running the viralrecon 2.6.0 on some sars-cov-2 sequences; I noticed that ivar.tsv output doesn't match with the snpeff. annotated vcf as well as the variant long table when there is polymorphism. I have attached the output. also to visualize things easier
Here is the snpeff vcf file, there is only one mutation at position 23606
When looking at the tsv file, there is two variants at the same mutation.
I try to add the command in the config file but doesn't fix the issue. withName: 'IVAR_VARIANTS_TO_VCF' {
ext.args = params.protocol == 'amplicon' ? '--ignore_strand_bias --ignore_merge_codons' : '--ignore_merge_codons'
}
I would appreciate if people can take a look and help me solve it. Thank you!
Description of the bug
I am recently running the viralrecon 2.6.0 on some sars-cov-2 sequences; I noticed that ivar.tsv output doesn't match with the snpeff. annotated vcf as well as the variant long table when there is polymorphism. I have attached the output. also to visualize things easier
![Screenshot 2024-05-13 at 12 49 47 PM](https://private-user-images.githubusercontent.com/97980830/330156167-c9e3b4ce-ac06-471a-a342-f9b9e8f82b04.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.T3vdKcewZdtNRjbdUqnS1e_5lcuy9dAozAGUEkf6GzM)
![Screenshot 2024-05-13 at 12 51 27 PM](https://private-user-images.githubusercontent.com/97980830/330156581-5a62b447-3817-450d-8912-64d56236dad8.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MjQ5NzE4NjYsIm5iZiI6MTcyNDk3MTU2NiwicGF0aCI6Ii85Nzk4MDgzMC8zMzAxNTY1ODEtNWE2MmI0NDctMzgxNy00NTBkLTg5MTItNjRkNTYyMzZkYWQ4LnBuZz9YLUFtei1BbGdvcml0aG09QVdTNC1ITUFDLVNIQTI1NiZYLUFtei1DcmVkZW50aWFsPUFLSUFWQ09EWUxTQTUzUFFLNFpBJTJGMjAyNDA4MjklMkZ1cy1lYXN0LTElMkZzMyUyRmF3czRfcmVxdWVzdCZYLUFtei1EYXRlPTIwMjQwODI5VDIyNDYwNlomWC1BbXotRXhwaXJlcz0zMDAmWC1BbXotU2lnbmF0dXJlPTg4ZGViYWIzMTA0MWRlN2FkYjhlZTBhYjJmYWI4NmIwMTRlNDI1YWU0NzlmYmM3OTMxMDZkYzJhYTc2NmNjODImWC1BbXotU2lnbmVkSGVhZGVycz1ob3N0JmFjdG9yX2lkPTAma2V5X2lkPTAmcmVwb19pZD0wIn0.rrIoLnjtku7ub9TB0yPMo-LV3IDUiUUq6Q7wW1Lmk1I)
Here is the snpeff vcf file, there is only one mutation at position 23606
When looking at the tsv file, there is two variants at the same mutation.
I try to add the command in the config file but doesn't fix the issue. withName: 'IVAR_VARIANTS_TO_VCF' {
ext.args = params.protocol == 'amplicon' ? '--ignore_strand_bias --ignore_merge_codons' : '--ignore_merge_codons'
}
I would appreciate if people can take a look and help me solve it. Thank you!
Command used and terminal output
No response
Relevant files
stock-variant.zip
System information
No response
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