 bwa index bam_ref.fasta
 samtools faidx bam_ref.fasta
 bwa mem bam_ref.fasta bam_query.fasta > bam_align.sam
 samtools import bam_ref.fasta.fai bam_align.sam bam_align.bam
 samtools sort bam_align.bam bam_align.sorted
 samtools index bam_align.sorted.bam
