My data were generated by Hiseq2000. So I used -F ILMFQ during run novoalign. Should I still need to convert the quality scores to sanger before I used samtool pileup for SNP calling? thanks for all the comments
It doesn't depend so much on HiSeq versus GAIIx as which version of the pipeline you're using. HiSeq SHOULD be 1.3+, which does encode phred quality scores with an offset of 64. The best thing you can do is to confirm what version of the pipeline the core that generated your sequence is using.
If it is 1.3+, the option you used in NOVOALIGN is correct as it interally converts to phred, since samtools requires phred scaling. If it was the old format that used the log of the probability ratios you would need to use SLXFQ instead.