Peter Thanks for your help. Long explanation below, but for those of you trying to fix a lexicographically ordered BAM so that it can be used by GATK, here's the bottom line: - samtools reheader just changes the names of the contigs (bobschr1 becomes bigDNApieceA) in the header and in the reads - picard tools ReorderSam will rearrange the reads according to a reference genome; as long as the reference is numerically ordered, you'll get the BAM you need.
Long explaination: When I used samtools reheader to try to fix my BAM, the command line below gave me a non-nonsensical (i.e. usable) output: $ samtools reheader reheader.sam accepted_hits.bam > accepted_hits_reheader2.bam # reheader.sam is a SAM/TXT file with the # desired numerically sorted header # accepted_hits.bam is the BAM file with # the problematic lexicographically # sorted header # accepted_hits_reorder2.bam is the output # BAM with the "fixed" header Unfortunately, this process not only relabeled the header, but also renamed each of the reads: Thus, this: HWI-ST976:117:C00CUACXX:6:2207:15663:154327 0 chr1 15659 255 51M * 0 0... Became this: HWI-ST976:117:C00CUACXX:6:2207:15663:154327 0 chrM 15659 255 51M * 0 0... Which is not helpful. Joshua Theisen, MD-PhD Pediatric Resident Physician, PGY-3 St. Louis Children's Hospital -----Original Message----- From: Peter Cock [mailto:p.j.a.c...@googlemail.com] Sent: Tuesday, October 14, 2014 11:12 To: Joshua Theisen Cc: samtools-help@lists.sourceforge.net Subject: Re: [Samtools-help] samtools reheader causes terminal to flicker On Tue, Oct 14, 2014 at 5:03 PM, Joshua Theisen <joshua.thei...@gmail.com> wrote: > 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? Those flickering symbols are the output BAM file, like most samtools command the output defaults to stdout, so pipe it: samtools reheader reheader.sam > accepted_hits.bam I'm not sure what reheader did with the extra argument - if it was simply ignored that is probably a bug. Note this will not actually sort the records in the order you want. Why are you trying to do this anyway? Peter ------------------------------------------------------------------------------ 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
