提取bed区间内的reads
samtools view -bh -L target.bed bamfile.bam > target.bam
samtools view -hb bamfile.bam chr:start-end > target.bam
对bed区间进行window拆分
# 以300K为窗口,每个窗口间隔100K 分割bed
bedtools makewindows -g wgs.bed.txt -w 300000 -s 100000 > windows300k_step100k.bed
wgs.bed.txt
计算bed区间的深度,返回区间内覆盖碱基数
samtools bedcov yourbedfile.bed file1.bam