--meta and --minRatio options in Minimac4

[rozaimirazali]

Hi.

In the Michigan Imputation Server pipeline page (http://imputationserver.readthedocs.io/en/latest/pipeline/), the Minimac4 command is using --meta and --minRatio in Minimac4?

However, I cannot find that option when I install the Minimac4 from GitHub

[Santy-8128]

Yes they are. Are they not working for some reason ?

On Mar 18, 2018 4:07 AM, "rozaimirazali" [email protected] wrote:

Hi.

Do we have --meta and --minRatio in Minimac4?

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[qtnguyen01]

Hi, Could you please let me know where I can find the manual/documentation for options --meta and --minRatio in Minimac4?

I checked at this URL https://genome.sph.umich.edu/wiki/Minimac3_-_Full_List_of_Options but could not find this information.

Thank you,

[Santy-8128]

Sorry for the late reply.

We haven't made a detailed documentation page for the user options. Really sorry about that. We will get to it as soon as possible.

In the meantime, --meta option generates a separate file that can be used for meta-imputation (it is a method/tool that we are currently working on and testing, let me know if you would like to know more). Otherwise, you can ignore that option for now.

--minRatio option stands for the minimum ratio of the number of genotyped variants to the number of reference panel variants in each chunk. The default value is 0.01 and has been kept as a check just in case certain chunks have a very low coverage. If any chunk has coverage less than the value of --minRatio, the code will exit with an error message. The user can of course reduce the value to make the code run.

Please let me know if that helps and if there are any other questions.

Regards, Sayantan Das,

23andMe

On Wed, Jul 10, 2019 at 11:38 AM qtnguyen01 [email protected] wrote:

Hi, Could you please let me know where I can find the manual/documentation for options --meta and --minRatio in Minimac4?

I checked at this URL https://genome.sph.umich.edu/wiki/Minimac3_-_Full_List_of_Options but could not find this information.

Thank you,

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