I have a GFF3 file of variants from nextgen sequencing and want to find non-synonymous changes. Any suggestions?
One possible way would be:
1. Use tool "Compute an expression on every row" to extract the reference allele and sample allele from column 9 (attributes column) of the GFF3 file 2. Download some codons (see help for "mutate codons" tool for more info about this) 3. Use the "mutate codons" tool to mutate the codons with the variants extracted from the GFF file.
Here is the problem:- The help examples for the tool "compute an expression on every row" are very simplistic. This tool is much more powerful. Where can we find information about how to extract substrings with this tool?