Can anyone help me with an issue please?
I performed NGS sequencing of a custom panel (that I designed) from illumina (Truseq). Could you tell me which tools can I use to calculate the coverage in my desired regions? I tried GATK and bcftools but I can not do what I wanted.
Imagine I have 100 amplicons that I amplified for 95 samples, I would like to know how many reads there are per sample and per amplicon. Something like this:
sample1 sample2 sample3 amplicon1 100 45 20 amplicon2 0 10 5 amplicon2 80 57 90
I need to understand how the sequencing worked in my panel, if I have coverage in all amplicons or not.
Thanks in advance,