Question: Merge vcf files of structural variants
gravatar for ma17
8 months ago by
ma170 wrote:


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.


structural_variants merge vcf • 558 views
ADD COMMENTlink modified 8 months ago by WouterDeCoster38k • written 8 months ago by ma170
gravatar for WouterDeCoster
8 months ago by
WouterDeCoster38k wrote:

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.

ADD COMMENTlink written 8 months ago by WouterDeCoster38k

Thanks! Exactly what I was looking for

ADD REPLYlink written 8 months ago by ma170

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

ADD REPLYlink written 3 months ago by bi_Scholar0
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