Trouble with HWE p value

[Giordano_Souza]

Dear Jacobs,

By using the module of quality control I noticed that the P value for
the HWE is not appearing in the output for locus of the module
qc.summary (genotype summary statistics). I got around this problem
using the module qc.concordance, which compared my data set against
itself to get the P value.

I also tried to get the p-value for HWE through the command "-hwp",
but was also not returned any value.

Now appreciate that.

Cordially,

Giordano Souza

[Kevin Jacobs <jacobs@bioinformed.com>]

On Thu, Dec 4, 2008 at 4:37 PM, Giordano_Souza <jwo...@gmail.com> wrote:

By using the module of quality control I noticed that the P value for
the HWE is not appearing in  the output for locus of the module
qc.summary (genotype summary statistics). I got around this problem
using the module qc.concordance, which compared my data set against
itself to get the P value.

I also tried to get the p-value for HWE through the command "-hwp",
but was also not returned any value.

Hi Giordano,

Try running:

  glu qc.summary --hwp <your genotype file> -o locus_stats.txt

Note the two dashes (--hwp).  The online documentation doesn't show that clearly.

Best regards,

-Kevin

[Giordano Bruno]

Hi Jacobs,

 

Thank you very much,

I tried what you recommended and now it worked perfectly.

Actually online documentation in the command "-- hwp" presents a single dash and another single suggestion that would also indicate the need to use the command "-- hwp" to get p value in the output of locus.

 

Best Regards,

2008/12/5 Kevin Jacobs <jac...@bioinformed.com> <bioin...@gmail.com>

[Jacobs, Kevin (NIH/NCI) [C]]

I’m working to correct the online documentation—the source document has two dashes (--), but the HTML transformation system that I use mangles them.  I’ll post as soon as I have a work-around in place.

 

Thanks again,

-Kevin

 

<br

[Jacobs, Kevin (NIH/NCI) [C]]

I updated the documentation generation system to the latest version, regenerated the docs, and this bug is not fixed.  Long command line options (those that begin with --) now appear correctly.

 

-Kevin