Hello,
Within the HUPO PSI, we are devising novel proteogenomics data standards that
are extension to the SAM/BAM format housing mass spectrometry information (see
http://www.psidev.info/proBAM <http://www.psidev.info/proBAM>).
I’m testing interoperability with existing software tools using our proBAM
format.
Within the format we added an novel header line, holding information on the
annotation used:
@GA AS:ENSEMBL VN:85
The SAM format specification document
(http://samtools.github.io/hts-specs/SAMv1.pdf
<http://samtools.github.io/hts-specs/SAMv1.pdf>) mentions that this is allowed:
###### (from section 1.3)
Each header line begins with the character ‘@’ followed by one of the
two-letter header record type codes defined in this section. In the header,
each line is TAB-delimited and, apart from @CO lines, each data field follows a
format ‘TAG:VALUE’ where TAG is a two-character string that defines the format
and content of VALUE. Thus header lines match
/^@[A-Z][A-Z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ or /^@CO\t.*/.
######
Still this extra header line is dropped after merging with samtools (file used:
https://goo.gl/378YaB <https://goo.gl/378YaB>):
Case 1 (normal):
samtools sort -o PXD001524srt.bam PXD001524.bam (@GA header line in original
bam file)
samtools index PXD001524srt.bam
samtools view -h PXD001524srt.bam -o PXD001524srt.sam (@GA header line still
present)
Case 2 (force sort to generate multiple files and then merge):
samtools sort -m 1m -o PPXD001524srt_aftermerge.bam PXD001524.bam
samtools index PXD001524srt_aftermerge.bam
samtools view -h PXD001524srt_aftermerge.bam -o PXD001524srt_aftermerge.sam
(@GA header line MISSING)
In my opinion, this should not happen, or am I missing something.
Thanks for your feedback,
Best regards,
Gerben Menschaert
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
