+ ACC=AF086833
+ mkdir -p refs
+ REF=refs/AF086833.fa
+ BAM=align.bam
+ efetch -db=nuccore -format=fasta -id=AF086833
+ bwa index refs/AF086833.fa
+ samtools faidx refs/AF086833.fa
+ dwgsim refs/AF086833.fa simulated
+ R1=simulated.bwa.read1.fastq
+ R2=simulated.bwa.read2.fastq
+ bwa mem refs/AF086833.fa simulated.bwa.read1.fastq simulated.bwa.read2.fastq
+ samtools sort
+ samtools index align.bam
+ freebayes -C 10 -f refs/AF086833.fa align.bam