+ 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
+ bcftools mpileup -B -Ovu -f refs/AF086833.fa align.bam
[mpileup] 1 samples in 1 input files
+ bcftools call -vc -Ov genotypes.vcf
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid