calling snps with samtools on novoalign data

[rcorbett]

Hi,
I have aligned illumina data with novoalign (default parameters). I directed novoalign to create SAM output. From here I am using samtools pileup/varfilter to call the snps.

I see that the mapping qualities of novoalign are different than in maq/bwa. To account for this I have set the -M parameter of pileup to 160 (the highest value I have seen so far).
Has anyone else tried this combination of tools who might have more recommendations on which parameters to use?

thanks!

[lh3]

A mapping quality 160 is certainly overestimated. Option -M is to reduce the side-effect of such overestimated mapping quality. Please keep it as the default. I think samtools will work well with novoalign under the default option.