Preserve Case when Using FastaAlternateReferenceMaker
I had soft masked a FASTA file using BEDTools'
maskfasta and wanted to use this as input to
FastaAlternateReferenceMaker as well as a VCF file. I was suprised to see that
FastaAlternateReferenceMaker had undone all the soft masking and output all uppercase bases. I would like to be able to preserve the case of my input reference sequence.
My particular use case is as follows:
1) I had performed a read mapping against a reference genome
2) I called variants from this mapping to create a VCF
3) I soft masked bases which had zero coverage from my reads
4) I wanted to use the soft masked reference plus VCF to generate a new reference for my sample where the output would still contain the information about which bases had zero coverage from my sample.