第二步-samtools-得到.bam文件

(base) luoyang@DESKTOP-AO2ICCR:/mnt/d/AAA-台式机-LY-WorkSpace$ samtools sort -@ 12 -o aligned/105TRA/105TRA.sorted.bam aligned/105TRA/105TRA.sam

[bam_sort_core] merging from 24 files and 12 in-memory blocks...

最后生成105TRA.sorted.bam文件

第二步：Sort and convert the SAM files to BAM:

10samples：

samtools sort -@ 12 -o aligned/105TRA/105TRA.sorted.bam aligned/105TRA/105TRA.sam  

samtools sort -@ 12 -o aligned/108TRA/108TRA.sorted.bam aligned/108TRA/108TRA.sam

samtools sort -@ 12 -o aligned/112A/112A.sorted.bam aligned/112A/112A.sam

samtools sort -@ 12 -o aligned/113A/113A.sorted.bam aligned/113A/113A.sam

samtools sort -@ 12 -o aligned/114A/114A.sorted.bam aligned/114A/114A.sam

samtools sort -@ 12 -o aligned/122A/122A.sorted.bam aligned/122A/122A.sam

samtools sort -@ 12 -o aligned/124A/124A.sorted.bam aligned/124A/124A.sam

samtools sort -@ 12 -o aligned/126A/126A.sorted.bam aligned/126A/126A.sam

samtools sort -@ 12 -o aligned/127A/127A.sorted.bam aligned/127A/127A.sam

samtools sort -@ 12 -o aligned/130A/130A.sorted.bam aligned/130A/130A.sam

ls

---

16samples：

samtools sort -@ 12 -o aligned-16/17F24T/17F24T.sorted.bam aligned-16/17F24T/17F24T.sam  

samtools sort -@ 12 -o aligned-16/105TRA/105TRA.sorted.bam aligned-16/105TRA/105TRA.sam 

samtools sort -@ 12 -o aligned-16/109TRA/109TRA.sorted.bam aligned-16/109TRA/109TRA.sam  

samtools sort -@ 12 -o aligned-16/110A/110A.sorted.bam aligned-16/110A/110A.sam 

samtools sort -@ 12 -o aligned-16/113A/113A.sorted.bam aligned-16/113A/113A.sam

samtools sort -@ 12 -o aligned-16/114A/114A.sorted.bam aligned-16/114A/114A.sam

samtools sort -@ 12 -o aligned-16/120A/120A.sorted.bam aligned-16/120A/120A.sam

samtools sort -@ 12 -o aligned-16/121A/121A.sorted.bam aligned-16/121A/121A.sam

samtools sort -@ 12 -o aligned-16/122A/122A.sorted.bam aligned-16/122A/122A.sam

samtools sort -@ 12 -o aligned-16/124A/124A.sorted.bam aligned-16/124A/124A.sam

samtools sort -@ 12 -o aligned-16/126A/126A.sorted.bam aligned-16/126A/126A.sam

samtools sort -@ 12 -o aligned-16/136A/136A.sorted.bam aligned-16/136A/136A.sam

samtools sort -@ 12 -o aligned-16/140A/140A.sorted.bam aligned-16/140A/140A.sam

samtools sort -@ 12 -o aligned-16/143A/143A.sorted.bam aligned-16/143A/143A.sam

samtools sort -@ 12 -o aligned-16/153A/153A.sorted.bam aligned-16/153A/153A.sam

samtools sort -@ 12 -o aligned-16/154A/154A.sorted.bam aligned-16/154A/154A.sam