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

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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
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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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