Analysis of SNP in viral genome

[vitor]

I'm analyzing mutations (SNPs) in the genome of a ssDNA virus (virus X and Y)
I had sequenced the total DNA in Illumina plataform HiSeq 2000 and I got the reads in FASTA format.

I want:
The reads filtered;
The reads mapped in reference genome.

I need
A program or tool to discovered the SNPs among the genome with reliability;
or/and some statistics to apply them;
and a statistic method to explain when a viral DNA (virus X) is higher than viral DNA (virus Y) in the same organism (probably the virus X replies more than the other, because the virus X has higher coverage than virus Y).

Thanks!