If one position such as chr8:125976061-125976501, then the command is prety straight forward. In Linux:
samtools view -o out input.sam chr8:125976061-125976501
However I have many positions in a list file, is there a batch way to do it? The list file format likes
Chr start end 15 10000 20000 15 20000 30000 15 30000 40000 15 40000 50000
Thanks for help.