Quality Calibration: GApipeline 1.0

[dvh]

Hi,

Can I please ask what people are doing regarding getting calibrated base call quality scores from solexa?

We have a GAII. This is now generating 45bp PE reads. In the new version of the GApipeline (1.0) it is possible to use ELAND alignment from a control lane (e.g. PhiX) to calibrate quality scores and apply this to other lanes. This is OK, for up to 32bp reads, but we see ELAND (including eland_extended) gives a big jump in error rate after 32bp versus e.g. MAQ. So are these calibrated quality scores for positions 33-45bp really OK?

Or should we just use the uncalibrated scores? We running alignments in MAQ. Various of our applications e.g. SNP discovery, need a filter on base call quality.

thanks

david

[cgb]

sanger has a quality calibrator and a lot of Maq experience - try emailing [email protected].