I found some similar topics here and also on another forums, but I still don't know how to exactly calculate quality for each variation in VCF file.
Thanks for all your help!
For samtools and GATK, read the samtools paper. EDIT: Er.. autolink is breaking my link.
sorry about that - I changed the regexp - the error that you hit should be handled although others may creep up so I'll be watching to see if this causes more trouble than good
I am going just add this to improve our answered question statistics ;-)
As lh3 says the samtools paper has the answer