这个网址有详细的SNP calling 的教程，所用软件为BWA和samtools
bwa index Glycyrrhiza_inflata.fasta
bwa aln Glycyrrhiza_inflata.fasta /mnt/org/chlo_ing/Glycyrrhiza_inflata/data/TZTD180303484_H7FJMDMXX_L1_1.fq.gz > aln_Gly_1.sai
bwa aln Glycyrrhiza_inflata.fasta /mnt/org/chlo_ing/Glycyrrhiza_inflata/data/TZTD180303484_H7FJMDMXX_L1_2.fq.gz > aln_Gly_2.sai
bwa sampe Glycyrrhiza_inflata.fasta aln_Gly_1.sai aln_Gly_2.sai /mnt/org/chlo_ing/Glycyrrhiza_inflata/data/TZTD180303484_H7FJMDMXX_L1_1.fq.gz /mnt/org/chlo_ing/Glycyrrhiza_inflata/data/TZTD180303484_H7FJMDMXX_L1_2.fq.gz > aln_Gly.sam
samtools view -S -b aln_Gly.sam > aln_Gly.bam
samtools sort aln_Gly.bam Gly-sorted
samtools faidx Glycyrrhiza_inflata.fasta
samtools mpileup -g -f Glycyrrhiza_inflata.fasta Gly-sorted.bam > Gly-raw.bcf
bcftools view -bvcg Gly-raw.bcf > Gly-var.bcf
samtools mpileup -g -f Glycyrrhiza_inflata.fasta Gly-sorted.bam > Gly-raw.bcf
bcftools view -bvcg Gly-raw.bcf > Gly-var.bcf
以上为我提取叶绿体中SNP的过程，最终的vcf文件在处理过后可用CircosVCF可视化
我还没学会，待我琢磨琢磨。
