Adding the optional IH tag to SAM files

One of the major complaints about the 2 most often used aligners BWA and Bowtie is its failure to report the NH or IH tag.

The IH tag is an indicator of the number of stored alignments in the SAM file that contains the current query (i.e. the read). This is meaningful for multi-mapped reads if you want to know to how many locations the same read has been mapped (eg. assuming your Bowtie parameter "k" has been set to more than 1).

I've written an awk oneliner that will add this tag to your SAM file. What it does is to iterate the file twice, first to tabulate counts, and second to write the extra tag.

SAM file directionality

Understanding direction flags and how to extract them

• http://biobeat.wordpress.com/2013/03/14/separating-bam-files-to-forward-and-reverse-strand-files/
• http://biobeat.wordpress.com/2013/04/29/directional-rna-seq-part-1-extract-strand-information-from-sam-file/

 Paired-end specific discussion:

• http://ppotato.wordpress.com/2010/08/25/samtool-bitwise-flag-paired-reads/
• http://www.novocraft.com/wiki/tiki-index.php?page=Extracting+unmapped+reads+from+a+BAM+file+produced+by+novoalign

Useful samflag utility
http://picard.sourceforge.net/explain-flags.html