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Describe the bug
Mehari generally requires vcf files to not have multi-allelic variants, which can be removed by a bcftools norm call.
The current wrapper does this only when the input vcf file is also restricted to a given bed file, and the current mehari version (0.21.1) does not seem to fail on all multi-allelic variants, so it works. Soon, we will need to update the mehari version though.
To Reproduce
Steps to reproduce the behavior:
(Manually) update mehari version to >= 0.25.5
Run varfish-export step without using a bed file
Expected behavior
The mehari wrapper should always run bcftools norm.
The text was updated successfully, but these errors were encountered:
Describe the bug
Mehari generally requires vcf files to not have multi-allelic variants, which can be removed by a bcftools norm call.
The current wrapper does this only when the input vcf file is also restricted to a given bed file, and the current mehari version (0.21.1) does not seem to fail on all multi-allelic variants, so it works. Soon, we will need to update the mehari version though.
To Reproduce
Steps to reproduce the behavior:
Expected behavior
The mehari wrapper should always run bcftools norm.
The text was updated successfully, but these errors were encountered: