I am also doing SNP analyses, I used following commands which could be of your interest, please adjust the input parameters accordingly:
In the following commands I am comparing two samples, prep2 and prep3, in this example I already have mapped .bam files. In case you have a single sample or file, you may input the single file and check parameters accordingly.
nohup samtools mpileup -t DP -uv -Q 15 -f /media/Storage/Analysis/mm9/genome.fa /media/Storage/Data/bam/prep2.bam /media/Storage/Data/bam/prep3.bam -o prep2-3_mpileup.vcf & bcftools call -mv prep2-3_mpileup.vcf > Only_variations.vcf & bcftools filter -s LowQual -e '%QUAL<20 || DP<30' Only_variations.vcf > Qualt20DP30_flt.vcf grep -P "\tPASS\t" Qualt20DP30_flt.vcf > Qualt20DP30_flt.vcf.passed
After these filtering steps, you might be interested in figuring out which one of those SNPs are homozygous and heterozygous. This analysis can be done by grep out the 1/1 or 0/1 pattern in the last column of your vcf file. Please check the manual of VCFv4.2 for the description.
If you have any further questions, let me know.