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[Vcftools-help] using vcf-tools to find differences between vcf files
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From: Paul D. <pau...@gm...> - 2012-02-06 19:48:37
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Dear VCFtools folks,
I'm trying to use the vcf-isec command to find differences between two vcf.gz files, but get this error message:
pauls-MacBook-Pro:P110202 p.denny$ ./vcf-isec -c chr7-BALBOla-B6-variants-25MbGWASpeak.vcf.gz chr7-CBAOla-B6-variants-25MbGWASpeak.vcf.gz | ./bgzip -c > BALB-CBA-chr7-25Mb.vcf.gz
Can't exec "tabix": No such file or directory at Vcf.pm line 2155.
at Vcf.pm line 2155
The command "tabix -l chr7-BALBOla-B6-variants-25MbGWASpeak.vcf.gz" exited with an error. Is the file tabix indexed?
at Vcf.pm line 171
Vcf::throw('Vcf4_0=HASH(0x7f7f8182d568)', 'The command "tabix -l chr7-BALBOla-B6-variants-25MbGWASpeak.v...') called at Vcf.pm line 2156
VcfReader::get_chromosomes('Vcf4_0=HASH(0x7f7f8182d568)') called at ./vcf-isec line 228
main::vcf_isec('HASH(0x7f7f81828908)') called at ./vcf-isec line 12
I have attached the vcf.gz files and a screenshot of the directory in which they are kept. As you can see, tabix, gzip and vcf.pm are all in the same directory, so any help would be appreciated.
OOPS - forgot directory screenshot last time!
Best,
Paul
Mobile: +44-07922078038
E Mail: pau...@gm...
Web: http://www.thesmartcoachingcompany.com/smartblog/
Twitter: http://twitter.com/pauldennyuk
LinkedIn: http://linkd.in/giXwQj
On 2 Feb 2012, at 09:11, Sendu Bala wrote:
> Either include the directory that contains tabix in your PATH environment variable, or move the tabix executable to a directory that is already in your PATH.
>
> http://kb.iu.edu/data/acar.html
>
>
> On 1 Feb 2012, at 20:06, Paul Denny wrote:
>> Dear Quang & VCF Tools folks
>>
>> I'm now using the vcf-tools and would appreciate help with directory structure when using the perl script
>>
>> vcf-query
>>
>> to select a subset of data rows from a file.vcf.gz file. when I use it, I get these errors:
>>
>> pauls-MacBook-Pro:perl p.denny$ ./vcf-query /Volumes/MacExternal/P110202/WTCHG_26484.bam.vcf.gz -r chr4:66480073-66595329
>> Can't exec "tabix": No such file or directory at Vcf.pm line 217.
>> tabix -h /Volumes/MacExternal/P110202/WTCHG_26484.bam.vcf.gz chr4:66480073-66595329 |: No such file or directory
>> at Vcf.pm line 171
>> Vcf::throw('Vcf=HASH(0x7fe4fa828ff8)', 'tabix -h /Volumes/MacExternal/P110202/WTCHG_26484.bam.vcf.gz...') called at Vcf.pm line 217
>> Vcf::_open('Vcf=HASH(0x7fe4fa828ff8)', 'region', 'chr4:66480073-66595329', 'print_header', 1) called at Vcf.pm line 165
>> Vcf::new('Vcf', 'file', '/Volumes/MacExternal/P110202/WTCHG_26484.bam.vcf.gz', 'region', 'chr4:66480073-66595329', 'print_header', 1) called at ./vcf-query line 156
>> main::read_data('HASH(0x7fe4fa803ed0)') called at ./vcf-query line 12
>> pauls-MacBook-Pro:perl p.denny$
>>
>>
>> it looks like the vcf-query script is trying to find the tabix executable, but is not looking in the correct directory. how should I either structure the directories, or edit the script(s) to 'know' where to look?
>>
>> NB I'm a complete newcomer to perl scripting...
>>
>> many thanks,
>>
>> Paul
>>
>> Mobile: +44-07922078038
>> E Mail: pau...@gm...
>> Web: http://www.thesmartcoachingcompany.com/smartblog/
>> Twitter: http://twitter.com/pauldennyuk
>> LinkedIn: http://linkd.in/giXwQj
>>
>>
>>
>>
>> On 18 Jan 2012, at 04:25, Quang Trinh wrote:
>>
>>> - Download tabix
>>>> tar xvjf tabix-0.2.5.tar.bz2
>>>> cd tabix-0.2.5
>>>> make
>>>> ./tabix
>>>
>>> see http://samtools.sourceforge.net/tabix.shtml on how to use tabix.
>>>
>>> Q
>>>
>>> On Fri, Jan 6, 2012 at 8:05 AM, Paul Denny <pau...@gm...> wrote:
>>>> Dear SAM tools guys / gals
>>>>
>>>> I am a Unix newbie, wanting to use tabix and bgzip from SAM tools to
>>>> compress and index some .VCF files. I've downloaded tabix-0.2.5 from here:
>>>>
>>>> http://sourceforge.net/projects/samtools/files/tabix/
>>>>
>>>> and also tried reading this:
>>>>
>>>> http://samtools.sourceforge.net/tabix.shtml
>>>>
>>>> about tabix, but do not know what to do with the downloaded files - what do
>>>> they need to be run on a Mac OS X (10.5.8) version of Unix? If so, please
>>>> point me at advice.
>>>>
>>>>
>>>> Best regards,
>>>>
>>>> Paul Denny
>>>>
>>>> Mobile: +44-07922078038
>>>> E Mail: pau...@gm...
>>>> Web: http://www.thesmartcoachingcompany.com/smartblog/
>>>> Twitter: http://twitter.com/pauldennyuk
>>>> LinkedIn: http://linkd.in/giXwQj
>>>>
>>>>
>>>>
>>>>
>>>>
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>>
>>
>> ------------------------------------------------------------------------------
>> Keep Your Developer Skills Current with LearnDevNow!
>> The most comprehensive online learning library for Microsoft developers
>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
>> Metro Style Apps, more. Free future releases when you subscribe now!
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>> _______________________________________________
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>
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