SVanalyzer
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nhansen
Tools for the analysis of structural variation in genomes
Hi there, I'm looking for a good method to combine calls produced by short variant callers (50bp). Most structural variant merging tools are designed to merge SVs from different SV...
Hi @nhansen, I am going through a SVWIDEN output of HG002 VCF. I have noticed that there are some variants that were annotated REPTYPE=CONTRAC has longer ALT than REF. I...
Hi @nhansen, I can't tell from the documentation exactly what the `--normshift` option does. It seems that `--maxdist` ensures two variants are near one another, `--normsizediff` ensures they're approximately the...
Hi nhansen, I recently tried SVmerge command to merge my SV vcfs. I found that in deletion, SVmerge can't merge variants with DEL tags correctly (even if they all have...
I want to use SVwiden to expand my VCF file, and I have ~9000 SVs, but the result file widened.vcf only got ~1000 SVs. The log file reported 2020/11/17 17:09:12...
While I'm thoroughly enjoying the robustness of your tool's clustering (thank you!), I thought I might make a feature request. Sniffles (https://github.com/fritzsedlazeck/Sniffles) calls SVs from long reads, and outputs a...
Hi there, For testing, I made two vcf files, one file has record like this chr1 108190704 DEL00000334 T \ . PASS IMPRECISE;SVTYPE=DEL;SVLEN=-3926;SVMETHOD=EMBL.DELLYv0.8.1;CHR2=chr1;END=108194630 ... and another file has only one...
