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From: Paul D. <pau...@gm...> - 2012-02-01 20:07:04
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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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