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Re: [Vcftools-help] using vcf-tools to convert between different versions of vcf files (3.3 to 4.0)
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From: Laura C. <la...@eb...> - 2012-03-06 16:37:01
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Okay this suggests that for some reason the vcf file you are using
does not have a header.
I haven't looked at this files myself so I am not sure if this is the
problem or if the error is indiciative of another problem
Are you running tabix yourself? do you use -h?
thanks
Laura
On Tue, Mar 6, 2012 at 10:31 AM, Paul Denny <pau...@gm...> wrote:
> Dear Laura
>
> thx for the advice, I've now done that, but am now getting these errors:
>
> zcat: /Volumes/MacExternal/WTSI-17Genomes/20111102-snps-all.annotated.vcf.gz.Z: No such file or directory
> Broken VCF header, no column names?
> at /Applications/vcftools_0.1.7/perl//Vcf.pm line 171
> Vcf::throw('Vcf4_1=HASH(0x7faa6b930b38)', 'Broken VCF header, no column names?') called at /Applications/vcftools_0.1.7/perl//Vcf.pm line 845
> VcfReader::_read_column_names('Vcf4_1=HASH(0x7faa6b930b38)') called at /Applications/vcftools_0.1.7/perl//Vcf.pm line 589
> VcfReader::parse_header('Vcf4_1=HASH(0x7faa6b930b38)') called at /usr/bin/vcf-convert line 63
> main::convert_file('HASH(0x7faa6b803ed0)') called at /usr/bin/vcf-convert line 12
> <rnal/WTSI-17Genomes/20111102-indels-all.annotated.vcf.gz chr7:24890278-25390278 > chr7-17genomes-25Mbpeak-indels.vcf
>
> Which suggests that it does't like the header, but I don't know what to try next - the original files can be viewed here:
>
> ftp://ftp-mouse.sanger.ac.uk/current_snps/20111102-snps-all.annotated.vcf.gz
> ftp://ftp-mouse.sanger.ac.uk/current_snps/20111102-snps-all.annotated.vcf.gz.tbi
>
> 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 5 Mar 2012, at 14:55, Laura Clarke wrote:
>
>> 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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>>>>
>>>>
>>>>
>>>> --
>>>> The Wellcome Trust Sanger Institute is operated by Genome Research
>>>> Limited, a charity registered in England with number 1021457 and a
>>>> company registered in England with number 2742969, whose registered
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