Samtools index doesn't work with a chromosome longer than 512Mbp. Heng
On Dec 16, 2014, at 11:41, olivier.rue <olivier....@toulouse.inra.fr> wrote: > Hello, > > I got an error when indexing my sorted BAM file. > > > samtools index file.bam > [E::hts_idx_push] NO_COOR reads not in a single block at the end 0 -1 > > I tried to check the validity of the file with picard-tools: > > > java -jar ValidateSamFile.jar I=file.bam IGNORE_WARNINGS=true > ERROR: Record 90709, Read name seq40369#11#7696, The record is out of > [coordinate] order, prior read name [seq28047#7#2353], prior coodinates [-1:0] > > The start coordinate of this read is higher than 1 billion: > > seq40369#11#7696 272 chrUn 1024548131 1 27M * 0 0 > GTTGTCTCTGATTCAGAATCATACTTA IIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 > XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:27 YT:Z:UU > > I retrieved identical problems with bedtools... > > Do you have already encountered this bug ? > > Thanks, > Olivier > > -- > ======================================================== > Olivier RUÉ > INRA - MIAT - Plateforme Bioinfo-Genotoul > Chemin de Borde-Rouge - Auzeville - CS 52627 > 31326 Castanet-Tolosan cedex - FRANCE > Tel: +33 (0)5.61.28.55.49 > > http://www.bioinfo.genotoul.fr/ > ------------------------------------------------------------------------------ > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server > from Actuate! Instantly Supercharge Your Business Reports and Dashboards > with Interactivity, Sharing, Native Excel Exports, App Integration & more > Get technology previously reserved for billion-dollar corporations, FREE > http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk_______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help ------------------------------------------------------------------------------ Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
