关于SNP

网址：https://www.ebi.ac.uk/sites/ebi.ac.uk/files/content.ebi.ac.uk/materials/2014/140217_AgriOmics/dan_bolser_snp_calling.pdf

这个网址有详细的SNP calling 的教程，所用软件为BWA和samtools

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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。