I am thinking of using Mpileup from Samtools to get the information on the read quality and read depth from the BAM files. In that case which script should I use?
I have been recommended the script below:
ref=my_fasta.fasta samtools mpileup -f $ref -r chromosome_1:1018000-1018100 my_bam.bam my_bam2.bam
P.S. I dont have to do Variant calling, just need the read information.
Thanks in advance for your help.