"""
echo "${meta.id}" > sample_name.list
bcftools mpileup \\
    --fasta-ref $fasta \\
    $options.args \\
    $bam \\
    | bcftools call --output-type v $options.args2 \\
    | bcftools reheader --samples sample_name.list \\
    | bcftools view --output-file ${prefix}.vcf.gz --output-type z $options.args3
tabix -p vcf -f ${prefix}.vcf.gz
bcftools stats ${prefix}.vcf.gz > ${prefix}.bcftools_stats.txt
echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
"""