MAQ analysis Illumina

[m_elena_bioinfo]

Hi,
I'm using MAQ.
Someone could tell me how can I evaluate the heterozygosity coverage in output file (.snp) and what is the READ DEPTH?
Thank you!
Maria Elena

[Jonathan]

Easy:
Do a maq pileup <chr.bfa> <align.map> and have the read depth annotated in your 4th column!

If you use the -v mode from pileup (see manual or simply 'maq pileup') you can also have a look at the heterozygosity - manually or with some script.

Just have a closer look on the pileup options and stuff.
Best
-Jonathan