/Users/miskodzamba/research/bwa/bwa-0.7.4/bwa index ref.fa
sleep 0.5
/Users/miskodzamba/research/bwa/bwa-0.7.4/bwa aln ref.fa ls_f_reads.fq > ls_f_reads.sai
sleep 0.5
/Users/miskodzamba/research/bwa/bwa-0.7.4/bwa aln ref.fa ls_r_reads.fq > ls_r_reads.sai
sleep 0.5
/Users/miskodzamba/research/bwa/bwa-0.7.4/bwa sampe ref.fa ls_f_reads.sai ls_r_reads.sai ls_f_reads.fq ls_r_reads.fq > mapped.sam
cat mapped.sam | samtools view -Sb -o mapped.bam -
samtools sort mapped.bam mapped_sorted
samtools index mapped_sorted.bam
