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Re: [Vcftools-help] using vcf-tools to find differences between vcf files
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From: Petr D. <pd...@sa...> - 2012-02-07 09:36:29
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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 > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> ------------------------------------------------------------------------------ > >>>> Keep Your Developer Skills Current with LearnDevNow! > >>>> The most comprehensive online learning library for Microsoft developers > >>>> is just $99.99! 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