Merge vcf files of structural variants

Question

[ma17]

Hi,

I have many single sample vcf files containing structural variants. I'm trying to merge all the vcfs to one multi-sample vcf, however as the breakpoints of structural variants are only estimates, the position of the same structural variant in different samples would be slightly different. Is there a way to merge individual vcfs containing structural variants into one multi sample vcf? taking account for example a percentage of overlap to call structural variants in different samples as the same variant.

Thanks

Answer 1

[WouterDeCoster]

For that purpose I use SURVIVOR merge, which has a distance setting specifying the maximal difference between pairs of breakpoints (start1 vs start2 and end1 vs end2). As such it doesn't use a percentage of overlap, but it is also not requiring exact breakpoints.

About the percentage overlap the author of SURVIVOR said that he doesn't think it is correct that large SVs easier reach that minimal percentage, and therefore he just uses a distance. I believe he uses a distance of 1kb, but I commonly use 500bp.

[ma17]

Thanks! Exactly what I was looking for

[bi_Scholar]

When an overlap between vcf files A and B is found, which SV representation (i.e. which breakpoints) is reported by SURVIROR?

Answer 2

[Benbird]

There is one recently published method that could address this question: SV-Pop https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2718-4