a feature request (inter-chromosomal structural variants) for mason_variator

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Assessment

Difficulty
5/5
Estimated time
Over a week
Newbie friendliness
20/100
Issue type
Feature
Clarity
Needs clarification
Activity status
Stale
Tech stack
cpp
Domain
bioinformatics

Research direction

Start by reviewing mason_variator's existing intra-chromosomal event handling, which the issue identifies as the current implementation. Define how inter-chromosomal translocations and indels between chromosomes A and B should be represented, including positions and lengths relative to the original chromosomes; done means these events can be simulated and their mutation information reported.

Written by the indexing model from the issue text.

Description

feature/-request

I have used mason_variator to simulate different types of structural variants.
The problem is that I need simulations for inter-chromosomal translocations and indels given two chromosome A and B.
For instance, some sequences are selected from A and moved to B and information about this mutation would be like A[position with respect to the original A chromosome, length], B[position with respect to the original B chromosome, length].

I satisfied with the current implementation in terms of user-friendliness with respect to intra-chromosomal events.

Thanks in advance.

Dominant language
C++
Stars
502
Forks
172
No merged PRs in 30d

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