[dpryan]

You'll have a call for every read covering that site, note the depth column. While Phred scores are just log10 values, they're usually encoded in ASCII by first adding 33 to the Phred score. The information provided in a pileup won't be useful for splicing, but it could help with finding RNA editing and other modifications (at least if they're observable in sequencing). Whether you want to use the pileup or just the VCF is sort of up to you.

[Giffredo]

ok I understood the output that mpileup give me.

Now I think that should exist a "script" to translate the output.. I mean: if I have ....,. in the output it means I have 6 reads in total in that X position in which 5 reads are forward and 1 is reverse. I think that for a normal py script, to do this kind of translation could be easy..

[dpryan]

Yeah, that'd be pretty straight-forward to do in most languages. I should note that there is a C API for this whole process if you prefer that.

[Giffredo]

before starting to make a script, I tried VarScan..

Reading input from Pileup_merge.pileup (VARSCAN)
chrM 1 G 4 3 G:3:1:21:1:0:3:0
chrM 2 G 4 4 G:4:1:24:1:0:4:0
chrM 3 A 4 4 A:4:1:24:1:0:4:0
chrM 4 T 4 3 T:3:1:23:1:0:3:0
chrM 5 C 2 1 C:1:1:24:1:0:1:0
chrM 6 C 4 3 C:3:1:23:1:0:3:0

mpileup file:
chrM 1 G 4 ^*,^7,^7,^*, 5529
chrM 2 G 4 ,,,, 7;8=
chrM 3 A 4 ,,,, 7:7=
chrM 4 T 4 ,,,, 465=
chrM 5 C 2 ,, 19
chrM 6 C 4 ,,,, 465=

A part that VARSCAN give me error after 300 positions (I ll think after about this error), I don t see the link between these 2 output..

[dpryan]

You might consider starting another thread. I'm unfamiliar with varscan's output and you're more likely to find someone who is if you start a thread mentioning varscan in the subject.

[Giffredo]

Ok, I think it is a good idea..

Anyway thank dpryan for all your suggests. I appreciated them so much