BAM/SAM files describe the alignment of the short reads on the reference. There is no statistics about the probability Zygosity of the allele here.

However, using samtools view, you can visualize your reads at a given position or extract the zygosity of your mutation using samtools pileup

http://samtools.sourceforge.net/

GATK UnifiedGenotyper with genotype option can generate it:

java -Xmx4000m [?] -jar $gatk <br> -R $REF <br> -T UnifiedGenotyper <br> -I subject.bam <br> --DBSNP $DBSNP <br> --out snps.vcf <br> -stand_call_conf 30.0 <br> -stand_emit_conf 10.0 <br> -l INFO <br> -A HaplotypeScore <br> -L $ExonFile <br> -U ALLOW_UNINDEXED_BAM <br> --genotype[?]