+ ACC=AF086833
+ SRR=SRR1553500
+ mkdir -p refs
+ REF=refs/AF086833.fa
+ BAM=SRR1553500.bam
+ efetch -db=nuccore -format=fasta -id=AF086833
+ seqret -filter -sid AF086833
+ bwa index refs/AF086833.fa
+ samtools faidx refs/AF086833.fa
+ fastq-dump -X 100000 --split-files SRR1553500
+ R1=SRR1553500_1.fastq
+ R2=SRR1553500_2.fastq
+ TAG='@RG\tID:SRR1553500\tSM:SRR1553500\tLB:SRR1553500'
+ bwa mem -R '@RG\tID:SRR1553500\tSM:SRR1553500\tLB:SRR1553500' refs/AF086833.fa SRR1553500_1.fastq SRR1553500_2.fastq
+ samtools sort
+ samtools index SRR1553500.bam
+ bcftools mpileup -Ovu -f refs/AF086833.fa SRR1553500.bam
[mpileup] 1 samples in 1 input files
+ bcftools call -vm -Ov genotypes.vcf
+ freebayes --ploidy 1 -f refs/AF086833.fa SRR1553500.bam