Good afternoon, I'm working with target capture sequencing and I would like to know the coverage of my target genes, which I just have in fasta format. I already have my reads aligned into the genome and in bam format and I also already did the SNP calling (with freebayes). So my questions are: - How can I calculate the coverage of my target genes in the bam files I have? - Could be a way to just do the SNP calling of those genes?
I'm aware that with bedtools I could calculate the coverage, but is asking me a bed file that I don't have.
Any type of help will be apreciate it, thanks!