Question: Ti Tv ratio and their usefulness in exome sequencing
4
gravatar for mangfu100
2.4 years ago by
mangfu100530
Korea, Republic Of
mangfu100530 wrote:

Hi all.

I am a beginner in the bioinformatics and I have some questions.

When I read some papers regarding the mutational landscape, nearly all of them described the Ti Tv ratio in terms of mutation spectrum with some pretty figures. Therefore I would like to apply this statistics to my research but I couldn't find its definition in a easy way and how to calculate it. Also, I have read some articles that nowadays ti/tv ratio has little impact when it comes to analyzing exome sequencing.

Therefore, I would like to ask you the following questions:

1) Ti Tv ratio: how to calculate it? Is there a website or tools that get them in an automatic way? If not, what should I know before writing some codes by myself?

2) for exome sequencing, all the things are equally applied when analyzing whole genome sequencing data?

sequencing next-gen genome • 5.2k views
ADD COMMENTlink modified 2.4 years ago by Evgeniia Golovina820 • written 2.4 years ago by mangfu100530
9
gravatar for Evgeniia Golovina
2.4 years ago by
Russia
Evgeniia Golovina820 wrote:

Hi!

The Ti/Tv ratio is simply the ratio of the number of transitions to the number of transversions for a pair of sequences. There is a worked example of this calculation on the snpSift homepage that may clarify this point.

1) VariantEval and SnpSift can be used to calculate the transition transversion (Ti/Tv) ratios.

2) Yep. According to literature survey, the Ti/Tv ratio should be approximately 2.1 for whole genome sequencing and 2.8 for whole exome sequencing. If you have a mix of non-exonic and exonic data and you don't have a whole genome then you can get Ti/Tv somewhere between 2.1 and 2.8.

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Evgeniia Golovina820
1

Just to add to the answer above that Ti/Tv ratio of 2:1 for whole genome sequencing generally represents spontaneous and neutral mutation. 

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Ashutosh Pandey11k
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