I am trying to extract the reads falling into the particular region from a bam file. I am using the following command:
samtools view -b out.bam "chr10:regionstart-regionend" > region.bam
When I run this command I only get one read into the output. However, I can see many reads mapping in that particular region when I visualize the alignment in IGV.
Could someone help me identify what am I doing wrong?
Thank you in advance