Re: [Vcftools-help] report of bug

[Laurie S. <lst...@gm...>]

I updated this afternoon and the problem was corrected. Thanks.

On Fri, Mar 30, 2012 at 1:10 AM, Adam Auton <ada...@gm...> wrote:
> 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
>>
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>
>
> --
> 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
>
>
>
>



-- 
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