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Option to generate consensus with BCFTools / BEDTools using iVar variants #246

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saramonzon opened this issue Jan 11, 2022 · 2 comments
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Option to generate consensus with BCFTools / BEDTools using iVar variants #246

saramonzon opened this issue Jan 11, 2022 · 2 comments
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@saramonzon @svarona
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enhancement Improvement for existing functionality
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2.3

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@saramonzon
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Is your feature request related to a problem? Please describe

ivar consensus command has some issues already reported in their github: andersen-lab/ivar#103 , andersen-lab/ivar#97, andersen-lab/ivar#85

Describe the solution you'd like

We want an alternative method for generating the consensus using ivar variants and bcftools consensus. We'll select variants with AF > threshold and include them in the consensus, and we'll mask the consensus fasta as for bcftools caller.
@saramonzon saramonzon added the enhancement Improvement for existing functionality label Jan 11, 2022
@saramonzon saramonzon added this to the 2.3 milestone Jan 11, 2022
@drpatelh
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Refactoring fixed in #260 so we now have options to use either --consensus_caller ivar or --consensus_caller bcftools.

@svarona is going to add bcftools filter in a follow up PR to filter the variants.

@drpatelh drpatelh changed the title New options --ivar-consensus or --bcftools-consensus using ivar variants output and a threshold. Option to generate consensus with BCFTools / BEDTools using iVar variants Jan 26, 2022
@drpatelh
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Follow up fixes in #264 #265

@svarona svarona mentioned this issue Feb 8, 2022
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@saramonzon saramonzon mentioned this issue Feb 9, 2022
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@saramonzon @drpatelh @svarona