bwa index Brachypodium_distachyon_Bd21.main_genome.scaffolds.fasta
bwa aln Brachypodium_distachyon_Bd21.main_genome.scaffolds.fasta kazu1_5TIR_A11.fa > brachy_kazu1_5TIR_A11.bwa
bwa samse Brachypodium_distachyon_Bd21.main_genome.scaffolds.fasta brachy_kazu1_5TIR_A11.bwa kazu1_5TIR_A11.fa  > brachy_kazu1_5TIR_A11.sam
less brachy_kazu1_5TIR_A11.sam 
samtools
samtools import Brachypodium_distachyon_Bd21.main_genome.scaffolds.fasta brachy_kazu1_5TIR_A11.sam  brachy_kazu1_5TIR_A11.bam
wc brachy_kazu1_5TIR_A11.bam
samtools sort brachy_kazu1_5TIR_A11.bam brachy_kazu1_5TIR_A11.bam.sorted
samtools pileup -f Brachypodium_distachyon_Bd21.main_genome.scaffolds.fasta brachy_kazu1_5TIR_A11.bam.sorted.bam  > brachy_kazu1_5TIR_A11.pileup
less brachy_kazu1_5TIR_A11.pileup