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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: Petr D. <pd...@sa...> - 2012-03-07 07:40:55
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Hi Paul,
what is the command line you are running and have you tried with the
latest version of VCFtools? Before reporting errors it is advisable to
check the latest SVN revision first.
What platform are you running this on? Zcat on Mac OS likes to
prepend .Z suffix to the argument which seems to be happening in your
case. The error you are observing is most likely that vcf-convert is not
able to read the VCF because of this. Older versions of VCFtools used
zcat but this was later changed to `gunzip -c` for compatibility
reasons. Upgrading to a newer version should help.
Best,
Petr
On Tue, 2012-03-06 at 16:31 +0000, Paul Denny 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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Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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