Re: [Vcftools-help] using vcf-tools to convert between different versions of vcf files (3.3 to 4.0)

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Hello Paul

You need to add the directory which contains the vcftools perl code to
your PERL5LIB env variable

thanks

Laura

On Mon, Mar 5, 2012 at 8:16 AM, Paul Denny <pau...@gm...> wrote:
> Dear VCF_tools folks
>
> thanks for help in the past.  I have now got tabix, bgzip, etc., working, but want to convert a VCF file from version 3.3 into v4.0 to extract some data.  I've tried using this command:
>
> zcat file.vcf.gz | vcf-convert -r reference.fa > out.vcf
>
> my starting file is called:
>
> 20111102-snps-all.annotated.vcf.gz
>
> and I've installed the various VCF tools in my
>
> /usr/bin
>
> directory, where tabix has worked for indexing VCF files and selecting subsets of data from within a compressed, indexed file,
>
> but I get this error message:
>
> zcat: /Volumes/MacExternal/WTSI-17Genomes/20111102-snps-all.annotated.vcf.gz.Z: No such file or directory
> Can't locate Vcf.pm in @INC (@INC contains: /Users/p.denny/Applications/vcftools_0.1.7/bin/ /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 /Network/Library/Perl/5.12/darwin-thread-multi-2level /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3 /System/Library/Perl/5.12/darwin-thread-multi-2level /System/Library/Perl/5.12 /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level /System/Library/Perl/Extras/5.12 .) at /usr/bin/vcf-convert line 6.
> BEGIN failed--compilation aborted at /usr/bin/vcf-convert line 6.
>
> Because I'm working only with SNPS, I have not included a FASTA format indexed reference sequence file in the command, because i believed it to not be obligatory and because I don't know where to get a mouse FASTA format indexed reference sequence.
>
> Suggestions, please!
>
> thanks,
>
> 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
>
>
>
>
> On 7 Feb 2012, at 09:36, Petr Danecek wrote:
>
>> Hi Paul,
>>
>> first of all, as described in the online documentation, bgzip (not gzip)
>> must be used to compress your VCFs. You should be able to run the
>> command shown in the error message below from the command line without
>> errors (tabix -l your.vcf.gz). If that does not work, then your
>> installation is messed up. The exact location of tabix binary does not
>> matter, but it must be in one of the search directories defined by the
>> PATH environment variable. This is a standard shell variable, please
>> google it up to learn more about this.
>> http://vcftools.sourceforge.net/docs.html
>>
>> By the way, you should address questions about VCFtools to the
>> vcftools-help mailing list only, samtools-help list is dedicated to,
>> well, samtools.
>> ;-)
>>
>> Best,
>> Petr
>>
>>
>> On Mon, 2012-02-06 at 17:03 +0000, Paul Denny wrote:
>>> 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.
>>>
>>> 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
>>>
>>>
>>>
>>>
>>> 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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