How can I calcualte the sequence identity and coverage form GMAP output bam file?

[huan]

Now I have got a bam file from gmap alignment with data from pacbio isoseq result. Now I want to get the statistic information about the coverage and identity of every sequence. So is there any tools can do the stat?Or How can I compute the identity and coverage form sam file?
Thanks a lot for reply!

[Brian Bushnell]

The BBMap package calculates both coverage and identity. For coverage, you can calculate it using a bam file with pileup.sh. Identity, however, requires alignment via BBMap (bbmap.sh) - just add the "idtag" flag, and all alignments will have an additional field indicating their percent identity, prefixed by "YI:f:". bbmap.sh can generate coverage and identity at the same time.