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is shorah same as lofreq? #87
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Not quite. LoFreq is mostly done position wise:
ShoRAH at its core is a local haplotype caller, SNVs are a by-product of this:
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Hi thanks again. thanks |
The flag to select is in the section The parameter for lofreq are taken from the section See the content of the file config/config.html in your local installation for a full reference of the configuration. |
thanks again,
looking at the config file suggested for sars cov 2 it seems no parameters are used to custom lofreq . while I believe these can be added , does it imply that lofreq is run in default - see screenshot
thanks
ibseq
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Sent: Thursday, October 6, 2022 12:25 pm
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Subject: Re: [cbg-ethz/shorah] is shorah same as lofreq? (Issue #87)
The flag to select is in the section general, parameter snv_caller.
The parameter for lofreq are taken from the section lofreq (example<https://github.com/cbg-ethz/pangolin/blob/6159461d926c677b80060e5c9fd2496cf6af6ffa/working/vpipe.config#L117>), unlike the parameters of shorah wich are taken from section snv (example<https://github.com/cbg-ethz/pangolin/blob/6159461d926c677b80060e5c9fd2496cf6af6ffa/working/vpipe.config#L123>)
See the content of the file config/config.html in your local installation for a full reference of the configuration.
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Hi all,
does shorah algorithms follow the same principle as lofreq?
thanks
Ibseq
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