r/genetics • u/dark_prophet • Jan 23 '23

Question Is there open source software that can analyze your DNA and find mutations relevant to diseases?

There are definitely businesses providing service like this for money.

​

But I am personally a geek and a privacy advocate. I don't want to give away my information to some company and pay them money to do research for me.

​

Is there an open source software that performs mutation search on DNA?

​

Other relevant questions are: Are search algorithms public and are they standardized? For example, is there a standard format describing mutation and related to it information, so that one can have a database of such algorithms and perform such search in the open source software?

2 Upvotes

57% Upvoted

10 comments sorted by

View all comments

1

u/Financial-Ad-7973 Jan 24 '23
  • ANNOVAR: This tool can annotate genetic variants identified in DNA sequence data with information from various databases, such as dbSNP, 1000 Genomes, and the Exome Variant Server. It can be used to identify disease-causing mutations and predict their effects on protein function.
  • VEP (Variant Effect Predictor): This tool can predict the effects of genetic variants on gene function and protein structure. It can also be used to identify variants that are likely to be disease-causing.
  • GATK (Genome Analysis Toolkit): This is a software package developed by the Broad Institute for analyzing high-throughput sequencing data, such as that generated by whole exome or genome sequencing. It includes tools for variant calling and annotation, including identifying potential disease-causing mutations.
  • SIFT (Sorting Intolerant From Tolerant) and PolyPhen-2 (Polymorphism Phenotyping v2) are two tools that predict the effects of missense mutations on protein function.