I'm new to this area. Sorry in advance if I say something inaccurately.
Now I have Raw Sequencing Data for many samples, and also a reference genome. For a given sample, I want to find out the depth of coverage (the number of reads that cover a given nucleotide) for all positions of SNPs in the reference genome. Is there any tools that I can use? I found that I can know the Read Depth using GATK HaplotypeCaller but only for the nucleotide having variants (genotype 0/1 or 1/1), which is lack of information for the 0/0 genotype.
Thank you in advance!