On Wed, 4 Jan 2017, John Marshall wrote:
> TL;DR i.e. what Rob said. But note that when you output SAM with >samtools view, samtools appends basic @SQ headers if there aren't already >any. So Rob's `samtools view -H ... | grep '^@SQ'` will display some >headers whether the file contains textual headers or not. Removing the >grep will allow some educated guesses to be made about whether @SQ >headers seen with samtools view are synthetic or really in the input >file: if there are any other (e.g. @RG) headers *after* the block of @SQ >headers, or if the @SQ headers have any fields beyond SN and LN, then >they are definitely real. Yes, I've just spotted this - samtools view fixes the problem too. Looking at the bam file with 'zless' might be the quickest way of checking for @SQ lines. The text header is fairly readable at the start. Rob Davies r...@sanger.ac.uk The Sanger Institute http://www.sanger.ac.uk/ Hinxton, Cambs., Tel. +44 (1223) 834244 CB10 1SA, U.K. Fax. +44 (1223) 494919 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ 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
