Scaling Bfast MQ to BWA MQ

[santy]

I am using Bfast to align SOLiD reads and BWA for illumina reads. I am calling SNPs and Indels using GATK, combining SOLiD and Illumina data.
However mapping quality for Bfast range from 0 to 255 while for BWA range is 0 to 70. for Bfast 255 is the best mapping quality but its considered as unreliable by GATK and filtred out. Is there any way of formula to scale Bfast MQs to BWA MQ.

Regards
Santosh

[nilshomer]

No one has generated such a function, but if you want to do so yourself, it is best to do it empirically by running both on the same dataset.