hi.. my aim is to convert snps to amino acid changes..
for calling snps i am using sam2tsv (https://github.com/lindenb/jvarkit/wiki/SAM2Tsv - a great tool by Pierre Lindenbaum ).. after that i want to see amino acid changes owing to codon changes.. for that i am parsing the sam2tsv output using matlab.. but as the matlab is very slow in doing that..
i wonder if there is any tool available.. that gives the information regarding amino acid/ codon changes from SNP calls..
eg. ref (A T G) to seq (G G A)
will give ref(M) to seq(G) ..
may be sam2tsv can be edited to give an option to do so.. :)
i have done sequencing of a single gene(600nts) carrying different amino acid mutations along the length of the gene.. i want to count the occurrence of mutations as depth per mutation.. how should i make the annotation file in this case? is snpeff applicable for this case?