Select 1

• Select the specific region in a Bam file.

$ samtools view -b myfile.bam chr1:10000-20000 > chr1.myfile.bam
$ ls
myfile.bam  chr1.myfile.bam

parallel samtools view -b {} chr1 ">" chr1.{/} ::: *.bam

Select 2

• Select the specific region from bed file.

$ samtools view -b myfile.bam -L exome.bed

Index

• It generates index files with bai suffix.

$ for i in *.bam;do samtools index $i;done
$ ls
myfile.bam  myfile.bam.bai

$ parallel samtools index ::: *.bam

Select & index

for i in {1..22} X Y; do mkdir chr$i; parallel samtools view -b {} chr$i ">" ./chr$i/chr$i.{/} ::: ../*.bam; parallel samtools index ::: ./chr$i/*.bam; done

Sort

$ samtools sort myfile.bam -o myfile.sorted.bam

Tview

$ samtools tview -p chr22 myfile.bam hg38.fa

22758816

• g : goto =10000
• http://blog.xyxu.top/2017-07-26-samtools-tview.html
• Underline : Secondary or orphan
• Base quality : Blue(0-9) Green(10-19), Yellow(20-29), White(>=30)

Extract

$ samtools view -b -h myfile.bam "chr22:10000-20000" > out.bam

Split fasta

$ samtools faidx hs38DH.fa chr1 > hs38DH_chr1.fa