Finding the Length Distribution of Structural Variations

Question

[Amirosein]

Hi

I am working on a simple algorithm to enable an aligner to handle structural variations, for the first step i need to know the distribution of the length of Structural Variations, for this purpose i need a database (or a reliable file)* providing structural variation information for me to calculate the distribution, anyone knows a database providing this for me? or any other way to this task?

the best thing i want is the estimated distribution but even knowing some statistics could be good, for example "90% of SVs are less than 200 bases long" or some other evident information like this.

the human genome SVs length Distribution will be good but having some wider information is better. *: update thanks everyone

[Pierre Lindenbaum]

for this purpose i need a database providing structural variation information for me to calculate the distribution, anyone

why do you need a database ? a simple text file and R would be enough , isn't it ?

[ivivek_ngs]

You just need the regions and calculate the length and plot the histogram in R for the column having the length, that is it.

[Amirosein]

yeah i need the regions, so where to get them?

[Amirosein]

yeah that could be good, but where?

[Pierre Lindenbaum]

"where" what ?

[Amirosein]

i need a simple text file and then do this in R :) i need that information then i know what to do with it :) now the problem is the data itself, ""where to find the length of Structural Variation?"" thanks

[Amirosein]

i need a simple text file and then do this in R :) i need that information then i know what to do with it :) now the problem is the data itself, where to find the length of Structural Variation? thanks

Answer 1

[Amirosein]

Poly Peak Parser will do it

published 2014 with this title:

Poly peak parser: Method and software for identification of unknown indels using sanger sequencing of polymerase chain reaction products.

it can find positions that deletions occurred in one of two sequenced strings

[Amirosein]

common! kidding me? polypeakparser is a software to find heterozygous indels in sanger reads but not for structural variation detection.