From: Akula, N. (NIH/N. [C] <ak...@ma...> - 2011-02-23 22:01:31
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ASSUME_SORTED=true command is not valid in GATK. I tried Picard sortsam.jar but got out of memory error. I am using >java -Xmx8g -jar picard/SortSam.jar I=sorted.bam O=coordinateSorted.bam SORT_ORDER=coordinate Thanks, Nirmala ------------------------------------------------------------------------------------ Nirmala Akula, MS, PhD Contractor, Human Genetics Branch NIMH/NIH Blg 35, Rm 1A/205 Bethesda, MD - 20892 Phone# 301-451-4258 ________________________________ From: Nils Homer [mailto:nil...@gm...] Sent: Wednesday, February 23, 2011 4:55 PM To: Akula, Nirmala (NIH/NIMH) [C] Cc: sam...@li... Subject: Re: [Samtools-help] sort order in Bam file 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...<mailto: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...<mailto:Sam...@li...> https://lists.sourceforge.net/lists/listinfo/samtools-help |