Question: Merge vcf files of structural variants
gravatar for ma17
2.1 years ago by
ma1710 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 • 1.7k views
ADD COMMENTlink modified 2.1 years ago by WouterDeCoster44k • written 2.1 years ago by ma1710
gravatar for WouterDeCoster
2.1 years ago by
WouterDeCoster44k 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 2.1 years ago by WouterDeCoster44k

Thanks! Exactly what I was looking for

ADD REPLYlink written 2.1 years ago by ma1710

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 20 months ago by bi_Scholar0
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