I have a bed file (list of SNPs of my interest).
I want to count the number of reads with mapping the reference sequence and variant sequence. Any suggestion on, which tools to use to retrieve this info ?
Different predictions tools like varscan, somaticSnipper have reported such number, but the number slightly varies. If possible, can this be done with GATK or sam/bamtools.
Thanks in advance !
PS: i added the answer, below.