Hello, I'm currently looking for an amino acid level variant caller for my data. I'm dealing with data that comes from saturation mutagenesis and, for any protein sequences analyzed, I am expecting each amino acid within the protein to be substituted for the 19 others (excluding start and stop codons). Each set of reads to be called includes up to 3 potential BP changes (as SNPs), one for each BP of the substituted amino acid. While it's possible to infer which AA is created after doing traditional BP calling, valuable QC information gets lost, (such as alt allelic frequency for each BP call, and zygosity callings.) I'm wondering if there's a variant caller available that works on the amino acid level. Generating the same statistics as a traditional caller, but instead, will take the fastq read files, and perform variant calling at the amino acid level.
Thanks! CJ Giacoletto