1.安裝samtools環(huán)境

sudo apt install samtools
samtools
samtools view

(安裝完成）

2. SAM格式轉(zhuǎn)為BAM格式

為參考基因組建立索引，生成了prefix.fai文件

samtools faidx GCA_000012525.1_ASM1252v1_genomic.fna
less GCA_000012525.1_ASM1252v1_genomic.fna.fai

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SAM2BAM

sam文件轉(zhuǎn)為bam文件

samtools view -bhS -t GCA_000012525.1_ASM1252v1_genomic.fna.fai -o PCC7942_bwa.bam PCC7942_bwa.sam #(最后這個sam文件用自己目錄的sam文件名)

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為bam文件排序，sort只能為bam文件排序，而不能為sam；不同版本samtools sort命令的-o參數(shù)不同

samtools sort PCC7942_bwa.bam -o PCC7942_bwa.bam.sorted
samtools index PCC7942_bwa.bam.sorted

統(tǒng)計比對結(jié)果

samtools depth PCC7942_bwa.bam.sorted>depth.txt
less depth.txt
samtools flagstat PCC7942_bwa.bam.sorted

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3. 查看比對結(jié)果

(1)samtools tview

samtools tview PCC7942_bwa.bam.sorted GCA_000012525.1_ASM1252v1_genomic.fna

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(2) artemis

https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/014/698/905/GCA_014698905.1_ASM1469890v1/GCA_014698905.1_ASM1469890v1_genomic.gff.gz
Open, GCA_000012525.1_ASM1252v1_genomic.fna文件

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Read an entry, GCA_000012525.1_ASM1252v1_genomic.gff

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Read Bam/vcf, PCC7942_bwa.bam.sorted （必須是排序、索引后的bam）

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4. BAM2BCF

samtools mpileup -f GCA_000012525.1_ASM1252v1_genomic.fna PCC7942_bwa.bam.sorted >bcf.txt
less bcf.txt

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samtools mpileup -gf GCA_000012525.1_ASM1252v1_genomic.fna PCC7942_bwa.bam.sorted>PCC7942_bwa.bcf
less PCC7942_bwa.bcf

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