Re: [Vcftools-help] report of bug

[Adam A. <ada...@gm...>]

I'm afraid I cannot replicate this error. Could you please confirm that you're using the latest version?

Kind regards,

Adam

vcftools --vcf valid-4.1.vcf --hwe 0.01

VCFtools - v0.1.8.1
(C) Adam Auton 2009

Parameters as interpreted:
	--vcf valid-4.1.vcf
	--max-alleles 2
	--hwe 0.01

Reading Index file.
File contains 10 entries and 3 individuals.
Applying Required Filters.
Filtering sites by number of alleles
Filtering sites by HWE p-value (only including bi-allelic sites)
After filtering, kept 3 out of 3 Individuals
After filtering, kept 8 out of a possible 10 Sites
Run Time = 0.00 seconds

On Mar 29, 2012, at 11:03 PM, Laurie Stevison wrote:

> Hello,
> 
> I'd like to report a bug in the --hwe option of vcftools. When you
> specify a value with a zero after the decimal, vcftools fails with the
> following error 'Error: Unknown option: 0.01'. If, however, you put an
> integer after the decimal, it runs just fine.
> 
> ex. I specified --hwe 0.01 and it failed, but with --hwe 0.1 it ran just fine.
> 
> Thanks,
> Laurie
> 
> -- 
> Laurie Stevison
> Institute for Human Genetics, UCSF
> http://www.duke.edu/~lss6/
> 
> 
> ~"Those who dare to fail miserably can achieve greatly." JFK~
> ~"I don't think that evolution is supremely important because it is my
> specialty; it is my specialty because I think it is supremely
> important." - GG Simpson
> 
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here 
> http://p.sf.net/sfu/sfd2d-msazure
> _______________________________________________
> Vcftools-help mailing list
> Vcf...@li...
> https://lists.sourceforge.net/lists/listinfo/vcftools-help


-- 
Adam Auton
Assistant Professor,
Department of Genetics,
Albert Einstein College of Medicine,
1301 Morris Park Avenue,
Price Center 320,
Bronx, New York 10461

Tel: +1 (718) 678 1038