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vatlab / vat-docs

Documentation for Variant Tools.
https://vatlab.github.io/vat/
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application -> association ->single gene ->cmc test #24

Open BingLi17 opened 6 years ago

BingLi17 commented 6 years ago 
vtools associate rare status -m "CFisher --name FisherMidP --alternative 1 --midp" --group_\
> by name2 --to_db cfisher -j8 > cfisher-midp.txt
INFO: Upgrading variant tools project to version 2.7.20
Verifying variants: 100% [===========================================] 26,797 66.3K/s in 00:00:00
INFO: 0 variants are updated
INFO: 3180 samples are found
Failed to locate field name2. Please use command "vtools show fields" to see a list of available fields.
BingLi17 commented 6 years ago 
     vtools associate rare status -m "RareCover --name RareCover -p 5000" --group_by name2 --to_\
>     db rarecover -j8 > rarecover.txt
usage: vtools associate --method RareCover [-h] [--name NAME] [-q1 MAFUPPER]
                                           [-q2 MAFLOWER] [-p N]
                                           [--adaptive C]
                                           [--moi {additive,dominant,recessive}]
vtools associate --method RareCover: error: unrecognized arguments: rarecover
HenryLeongStat commented 6 years ago

@gaow could you have a look? Is rarecover a real parameter?

gaow commented 6 years ago

@HenryLeongStat RareCover is name of a method but rarecover is the database name for outpout:

http://varianttools.sourceforge.net/Association/RareCover

At least it worked before as you can see in the example. Could you try without hte line break?