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

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

Dear Sendu

thanks very much for your help - it worked!

Best,

Paul

Mobile:    +44-07922078038
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On 2 Feb 2012, at 11:40, Sendu Bala wrote:

> You should have replied to the list, not to me only. But see my reply below.
> 
> On 2 Feb 2012, at 11:18, Paul Denny wrote:
>> Dear Sendu
>> 
>> thanks very much for the help -  I've tried to pull selected data from a local .vcf file that I downloaded for a specific genomic interval, but the new .vcf file written contains no data - only all the header rows, plus the column labels in a standard VCF4.0 file. My starting file uses the #CHR names chr1, chr2, etc rather than 1, 2, 3, etc., which I've allowed for, so I'm stuck. any ideas welcomed.
>> 
>> NB this is the command I used:
>> 
>> ./tabix -fh /Users/p.denny/Documents/Gene-Effects/vcftools_0.1.7/examples/subset.vcf.gz 1:100-160 > subset-chr1.vcf
> 
> It worked fine for me. -f is extraneous here btw.
> 
> 
>> What am I doing wrong?
> 
> I'm guessing you indexed your vcf file incorrectly. Do:
> tabix -fp vcf subset.vcf.gz
> 
> 
> 
>> 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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>>> 
>> <subset.vcf><subset.vcf.gz><subset-chr1.vcf>
>