Open ibseq opened 1 year ago
Not quite.
LoFreq is mostly done position wise:
ShoRAH at its core is a local haplotype caller, SNVs are a by-product of this:
Hi thanks again. I’m aware that we can use a flag to specifically use lofreq instead of shorah to analyse the data, in that case which parameters from Lofreq are then chosen?
thanks ibseq
The flag to select is in the section general
, parameter snv_caller
.
The parameter for lofreq are taken from the section lofreq
(example), unlike the parameters of shorah wich are taken from section snv
(example)
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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From: DrYak @.> Sent: Thursday, October 6, 2022 12:25 pm To: cbg-ethz/shorah @.> Cc: ibseq @.>; Author @.> 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 (examplehttps://github.com/cbg-ethz/pangolin/blob/6159461d926c677b80060e5c9fd2496cf6af6ffa/working/vpipe.config#L117), unlike the parameters of shorah wich are taken from section snv (examplehttps://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