Detect SNPs and indels with samtools mpileup and bcftools.

def run_samtools(align_bams, items, ref_file, assoc_files, region=None,
                 out_file=None):
    """Detect SNPs and indels with samtools mpileup and bcftools.
    """
    return shared_variantcall(_call_variants_samtools, "samtools", align_bams, ref_file,
                              items, assoc_files, region, out_file)