Create genomic databases with SIFT predictions. Input is an organism's genomic DNA (.fa) file and the gene annotation file (.gtf). Output will be a database that can be used with SIFT4G_Annotator.jar to annotate VCF files.
I am wondering how SIFT4G_Create_Genomic_DB handle lowercase nucleotides included in the genomic fasta .fa.gz and .vcf.gz input files? I would prefer to keep .fa.gz softmasked and the lowercase in .vcf.gz provides some additional information as well, but if sift4g does not take lowercases on its analysis I will convert to uppercase beforehand. Thank you.
Dear Pauline,
I am wondering how SIFT4G_Create_Genomic_DB handle lowercase nucleotides included in the genomic fasta .fa.gz and .vcf.gz input files? I would prefer to keep .fa.gz softmasked and the lowercase in .vcf.gz provides some additional information as well, but if sift4g does not take lowercases on its analysis I will convert to uppercase beforehand. Thank you.
Rom