bwa index reference.fasta
bwa mem reference.fasta reads_1.fq reads_2.fq > output.sam
samtools view -bS output.sam > output.bam
samtools sort output.bam -o output.sorted.bam
samtools depth output.sorted.bam > coverage.txt
bwa index reference.fasta
bwa mem reference.fasta reads_1.fq reads_2.fq > output.sam
samtools view -bS output.sam > output.bam
samtools sort output.bam -o output.sorted.bam
samtools depth output.sorted.bam > coverage.txt