Flagging Low Coverage Regions for Alternate Reference Maker
I am currently working on a comparative genomics project which involves using NGS datasets to map reads from several closely related species to a reference genome. I'd like to produce alternate fasta files for each species incorporating SNPs discovered using the GATK pipeline. Due to the experimental design I expect that there are regions in the genome that have low coverage, therefore I'd like to have a way to designate a base position as "N" if the read depth at that position does not meet a specified threshold. I found some tools to do diagnostic evaluation of coverage depth, but I couldn't find out a tool that would incorporate low coverage into the output fasta file produced by a tool such as FastaAlternateReferenceMaker. Thanks in advance!