Mapping SOLiD Reads using BFast.

[kasthuri]

I am new to using BFast. I was able to successfully install it. I now
have question regarding mapping the reads.

I have two SOLiD csfasta paired end files,

reads1.csfasta - 50 bp
reads2.csfasta - 35 bp

What is best way to align them using BFast for the human genome? If I
am using two separate commands how to merge them to obtain a single
bam/sam file?

I would want to use GATK pipeline for making SNP calls and so how do I
make sure that the aligned reads has good default base quality?

I would greatly appreciate the reply.

Thanks
-Kasthuri