I have reads (fastq data) of a particular gene from the human genome hg38. I also have the genbank (GBK) file and the fasta file of the gene of interest. I want to know what variants map to each exon of that gene and the coverage of each exon of that gene.
For example, I want to be able to say: variant T > A occurs at hg38 reference position chr12:88813734 which is exon 1/14 of the gene, variant TGGGA > TA occurs at hg38 reference position chr12:88847259 which is exon 5/14 of the gene, and so on. Exon 1 has 10000X coverage, Exon 2 has 11500X coverage, and so on.
Is there a variant caller that does this? If not, what protocol would you use to do this kind of analysis?
I understand not all variants reported will map to the exons. Is there a variant caller that will tell me the IVS that the variant maps to. For example, variant G > C occurs at hg38 reference position chr12:88846432 which is intron7 of the gene (IVS-7).