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karel-brinda / ococo

Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
https://arxiv.org/abs/1712.01146
MIT License
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Include deletion events in VCF #31

Open Takadonet opened 6 years ago

Takadonet commented 6 years ago

Hey was curious to know if deletion events will be included when calculation both AF and COV values in VCF? Below is an example where I would probably not call a SNV because of all the indel's found.

snv

Takadonet commented 6 years ago

So looks you can make them be included IF you set the minimum base pair quality to 0.

karel-brinda commented 6 years ago

Deletions are currently ignored as they can't be represented by the implemented counter configurations. However, I could add additional counters for deletions in some future version of Ococo.

Takadonet commented 6 years ago

That would be great! Thanks for the info.