[Vcftools-help] using tabix & vcf-tools to select a subset of data in vcf files

[Paul D. <pau...@gm...>]

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
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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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