Let's say you have some contig, X, and a list of SVs from Lumpy internal to X (i.e. no inter-contig TRA stuff). Could you then construct a new contig, X prime, that resolves or minimizes that list of SVs?
In other words, are there any tools that would take a Lumpy output file describing SVs internal to a single sequence (e.g. VCF, or any filetype that can be made from it) and output an updated version of the sequence that minimizes the number of listed SVs?
It seems like a graph-based problem that I assume has already been solved. It would minimally involve breaking up the contig into unit blocks and shuffling them around / reverse complementing as needed to minimize SV signals.
Hi @arq5x and others,
As usual, thanks for the great tool(s).
Let's say you have some contig, X, and a list of SVs from Lumpy internal to X (i.e. no inter-contig TRA stuff). Could you then construct a new contig, X prime, that resolves or minimizes that list of SVs?
In other words, are there any tools that would take a Lumpy output file describing SVs internal to a single sequence (e.g. VCF, or any filetype that can be made from it) and output an updated version of the sequence that minimizes the number of listed SVs?
It seems like a graph-based problem that I assume has already been solved. It would minimally involve breaking up the contig into unit blocks and shuffling them around / reverse complementing as needed to minimize SV signals.
Best,
John