From: Nils H. <nil...@gm...> - 2011-02-23 21:55:17
|
If you have sorted the file you can use "ASSUME_SORTED=true" or use "SortSAM.jar" to do the sorting. Nils On Wed, Feb 23, 2011 at 1:51 PM, Akula, Nirmala (NIH/NIMH) [C] < ak...@ma...> wrote: > Hi, > > > > I am using GATK to call SNPs in exome data and the program > gave an error message that BAM file is not co-ordinate sorted. I looked at > the header in the BAM file and it shows “SO:queryname”. > > > > I tried to use samtools reheader but that does not seem to > work. Here are commands: > > > > >Samtools view –H sorted.bam >myheader.txt > > > > >I edited myheader.txt by replacing “SO=queryname” to “SO=coordinate” in > EMACS > > > > >samtools reheader edited_myheader.txt sorted.BAM > > > > Thank you in advance for your responses. > > > > Regards, > > Nirmala > > > > > ------------------------------------------------------------------------------------ > > Nirmala Akula, MS, PhD > > Contractor, > > Human Genetics Branch > > NIMH/NIH > > Blg 35, Rm 1A/205 > > Bethesda, MD - 20892 > > Phone# 301-451-4258 > > > > > ------------------------------------------------------------------------------ > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > _______________________________________________ > Samtools-help mailing list > Sam...@li... > https://lists.sourceforge.net/lists/listinfo/samtools-help > > |