[maq-help] SNP filtering and calling

[Olivier H. <oh...@sc...>]

Hi,

I have question about the cns.final.snp output file from maq.pl easyrun.

What are the filters applied to the SNPs (depth/repeats/quality) ? Is  
there a way to play with the parameters ?

In the output, the last column (quality difference between strong and  
weak allele) doesn't make sense to me as the values go from -124 to  
124. Can you explain a little ?

thanks for your answer.

Olivier