I am extracting the reads from bam file which are falling in particular region using the following command.
samtools view -h input.bam "Chr10:18000-45500" > output.bam
However, now I want to extract the reads in sam manner but my reference is human genome primary assembly where the name of fasta reads starts like:
NC_000001.10 Homo sapiens chromosome 1, GRCh37.p13 Primary Assembly
How do I now modify command to do the sam task?
Thank you in advance.