I need help finding Stata programs for genetic studies

[Ela Nowakowska]

Hello everyone,

I have been searching for some Stata programs that I could use for my genetic studies data. So far I've found some written by Mario Cleaves, (genhw, hwsnp), Neil Shephard (genass) and David Clayton (ginsheet, gloci, gtab, htype). So far I have found and downloaded only Mario Cleaves' and Neil Shephard's programs, but I am running into some trouble.

I have missing genotype data and need to update genhw, but I don't know where to find or how to find the latest version of the program. I have tried "findit" but it tells me that I have the latest program installed, and the most I've been able to track for Cleave's updated program was here: https://www.stata.com/statalist/arch.../msg00006.html, which leads to http://biostat-resources.com/stata, which is a dead end.

As for Shepard's I understand that it requires some other programs to work properly, but I cannot find those programs using "findit" or by internet searching.

I cannot find any of David Clayton's program using "findit" at all, and on the internet I've found a link :http://www-gene.cimr.cam.ac.uk/clayt...ata/README.txt but that too seems to be broken.

I would be really grateful if anyone can help me find these programs, or know of any alternate programs that I can use. Basically, I have genotype data for various SNPs and some outcomes of interest, and would like to preform some basic association tests, and create/calculate LD and haplogroups.

Thanks,
Ela

[FernandoRios]

Hi Ela
Unless there is someone else in your same field who happens to have used and downloaded those programs in the past, chances are no one may be able to help.
My suggestion, however, is to contact the authors (if you haven't done so already), and ask for copies/
They may even have updated versions that for some reason they never uploaded anywhere else, or that found their programs too hard to follow to post them on SSC.
(I have done both)
HTH
F

[Ela Nowakowska]

Hi Ela
Unless there is someone else in your same field who happens to have used and downloaded those programs in the past, chances are no one may be able to help.
My suggestion, however, is to contact the authors (if you haven't done so already), and ask for copies/
They may even have updated versions that for some reason they never uploaded anywhere else, or that found their programs too hard to follow to post them on SSC.
(I have done both)
HTH
F

Thanks Fernando, I was actually hoping there may be some people where who have downloaded those programs and could share with me. I think they are relatively popular programs (Stata seems to be more for clinical rather than genetic research), and I think the authors are also on Statalist. I felt it might be rude to message them immediately without trying first :D

[Ela Nowakowska]

X

[Ela Nowakowska]

Bumping up my post as I think there may be someone in the forums who has these programs and can share or know how I can contact the authors!

[Nick Cox]

I have not downloaded any of these commands and can't speak to their current status. In essence I agree with FernandoRios to try contacting the authors.


All three authors appear to be research-active, For the record, the first author named is Mario A Cleves (not Cleaves or Cleave).and the second is Neil Shephard not Shepard (search Sheffield, not Harvard).

[Ela Nowakowska]

I have not downloaded any of these commands and can't speak to their current status. In essence I agree with FernandoRios to try contacting the authors.


All three authors appear to be research-active, For the record, the first author named is Mario A Cleves (not Cleaves or Cleave).and the second is Neil Shephard not Shepard (search Sheffield, not Harvard).

Thank you Nick! Maybe that's why I've been having some trouble finding them. I'll try this.