Sorry, forgot to include the command line from the Picard tool that worked:
java -jar /home/.../picard-tools-1.84.saved/ReorderSam.jar \
I= accepted_hits.bam \
O= accepted_hits_reordered.bam\
REFERENCE= /home/.../genome.fa \
Joshua Theisen, MD-PhD
Pediatric Resident Physician, PGY-3
St. Louis Children's Hospital
-----Original Message-----
From: Joshua Theisen [mailto:[email protected]]
Sent: Tuesday, October 14, 2014 14:43
To: 'Peter Cock'
Cc: '[email protected]'
Subject: RE: [Samtools-help] samtools reheader causes terminal to flicker
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:[email protected]]
Sent: Tuesday, October 14, 2014 11:12
To: Joshua Theisen
Cc: [email protected]
Subject: Re: [Samtools-help] samtools reheader causes terminal to flicker
On Tue, Oct 14, 2014 at 5:03 PM, Joshua Theisen <[email protected]>
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
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