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Example:
1. samtools mpileup -uf Euf reference.fna aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
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aln1.bam, aln2.bam : BAM files containing alignment results. You can use 1 or more alignment flies at a time. Note that as of late 2011, the new BAQ filter seems to aggressively remove SNPs unless you "extend" it with the "-E" option.
2. bcftools view var.raw.bcf | vcfutils.pl varFilter -D10 > var.filtered.vcf
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