I have a BAM with the @SQ lines of the header in lexigraphical order instead of numerical order:
***Have: @HD VN:1.0 SO:coordinate @SQ SN:chr1 LN:249250621 @SQ SN:chr10 LN:135534747 @SQ SN:chr11 LN:135006516 @SQ SN:chr12 LN:133851895 | | | @SQ SN:chr19 LN:59128983 @SQ SN:chr2 LN:243199373 @SQ SN:chr20 LN:63025520 @SQ SN:chr21 LN:48129895 @SQ SN:chr22 LN:51304566 @SQ SN:chr3 LN:198022430 | | | @SQ SN:chrM LN:16571 @SQ SN:chrX LN:155270560 @SQ SN:chrY LN:59373566 @PG ID:TopHat VN:2.0.0 ***Want: @HD VN:1.0 SO:coordinate @SQ SN:chr1 LN:249250621 @SQ SN:chr2 LN:243199373 | | | @SQ SN:chr9 LN:141213431 @SQ SN:chr10 LN:135534747 @SQ SN:chr11 LN:135006516 | | | @SQ SN:chr22 LN:51304566 @SQ SN:chrX LN:155270560 @SQ SN:chrY LN:59373566 @SQ SN:chrM LN:16571 @PG ID:TopHat VN:2.0.0 I'm trying to use samtools reheader using this pipeline: # extract header from BAM to SAM $ samtools view -H accepted_hits.bam > header.sam # manually edit header using vi, save as reheader.sam # replace header in orginal BAM file $ samtools reheader reheader.sam accepted_hits.bam When I do this I get flickering symbols in the PuTTY terminal and no change to the BAM. Any ideas? Thanks Josh Joshua Theisen, MD-PhD Pediatric Resident Physician, PGY-3 St. Louis Children's Hospital ------------------------------------------------------------------------------ Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
