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Re: [Samtools-help] Samtools-help Digest, Vol 104, Issue 1
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From: Stephane P. | V. | <ste...@vi...> - 2017-09-04 12:32:10
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Alan, Tom is right, it only works with bgzipped data sorted by chr and at least start-coordinate. BUT You can have these columns where you like in your tabular data, not necessarily in column 1 and 2 as found in bed/vcf files To handle more exotic column numbers, you can tune your tabix command tabix -h -0, --zero-based coordinates are zero-based -b, --begin INT column number for region start [4] -c, --comment CHAR skip comment lines starting with CHAR [null] -C, --csi generate CSI index for VCF (default is TBI) -e, --end INT column number for region end (if no end, set INT to -b) [5] ... -p, --preset STR gff, bed, sam, vcf -s, --sequence INT column number for sequence names (suppressed by -p) [1] … ALT when you use gff vcf bed or sam you have the -p argument to tell tabix what to expect Tabix is really amazing for searching through huge data files! S Stéphane Plaisance – Staff Scientist | Bioinformatician VIB Nucleomics Core Campus Gasthuisberg Herestraat 49 – Post Box 816 – 3000 Leuven – Belgium O&N4 Building – 8th Floor – Room 08.440 Tel. +32 16 37 31 26 Lync. +32 16 32 00 60 www.nucleomics.be <http://www.nucleomics.be/> <http://www.nucleomics.be/> <http://www.nucleomics.be/> <http://www.nucleomics.be/> <http://www.vib.be/> > On 04 Sep 2017, at 14:07, sam...@li... wrote: > > Send Samtools-help mailing list submissions to > sam...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/samtools-help > or, via email, send a message with subject or body 'help' to > sam...@li... > > You can reach the person managing the list at > sam...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Samtools-help digest..." > > > Today's Topics: > > 1. use tabix with multi-chromosome file (Alan Achenbach) > 2. Re: use tabix with multi-chromosome file (Thomas W. Blackwell) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 3 Sep 2017 19:28:38 +0000 > From: Alan Achenbach <ala...@ut...> > To: "sam...@li..." > <sam...@li...> > Subject: [Samtools-help] use tabix with multi-chromosome file > Message-ID: > <A27CC31880704940A9AF45B4405DF85E32D17565@X-MB9.xds.umail.utah.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Can tabix be used to index multi-chromosome files? What is used for begin and end if I have chromosome in column one and position in column two of a non-vcf file? > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 2 > Date: Sun, 3 Sep 2017 17:31:17 -0400 (EDT) > From: "Thomas W. Blackwell" <tb...@um...> > To: Alan Achenbach <ala...@ut...> > Cc: "sam...@li..." > <sam...@li...> > Subject: Re: [Samtools-help] use tabix with multi-chromosome file > Message-ID: > <alp...@me...> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Alan - > > Yes, tabix works fine for indexing and retrieval from > multi-chromosome files. It relies on the extra fields > provided by bgzip compression, not simply gzip. I think > it doesn't work on uncompressed files. The entries for > each chromosome must be sorted. Chromosome in column 1 > and position in column 2 should be close enough to .vcf > format so that tabix will work with no additional > arguments. Give it a try. > > - tom blackwell - > > On Sun, 3 Sep 2017, Alan Achenbach wrote: > >> Can tabix be used to index multi-chromosome files? What is used for begin and end if I have chromosome in column one and position in column two of a non-vcf file? >> > > > > ------------------------------ > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Samtools-help mailing list > Sam...@li... > https://lists.sourceforge.net/lists/listinfo/samtools-help > > > ------------------------------ > > End of Samtools-help Digest, Vol 104, Issue 1 > ********************************************* |