SVDB
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J35P312
structural variant database software
Hi, I think people are looking for SV merge tools often, and after testing many SV merge tools, such as `SURVIVOR`, `svimmer`, `SVanalyzer`, `svtools`, `truvari`, `bcftools`, and many other tools,...
Hi there! I'm using SVDB merge to combine some small cohorts of manta VCFs together, however I'm getting the following error: ``` svdb --merge --vcf b16/diploidSV.vcf.gz b15/diploidSV.vcf.gz b14/diploidSV.vcf.gz --bnd_distance 500...
Hello, I'd like to ask if there is a way of only keeping one INFO field when merging VCFs, meaning if there is a variant that is found by 2...
This is a little bit of a classic! Since it will not be obvious between runs what callers were combined for `set=Intersection` merges (found by all callers). The `FOUND_IN` tag...
Running `svdb v2.6.1` as: ``` svdb --merge --vcf cnvnat delly lumpy manta --pass_only --no_intra --no_var --overlap 0.1 --bnd_distance 1000 ``` and passing the output through `bcftools`, I am getting some...
Hi there, I just tested this tool for combining the outputs of Delly, Manta, and TIDDIT. It seems to work great! I'm not necessarily sure this is an issue and...
To code could use some refactoring. This is quite important, since it hopefully will encourage others to add new features. Refactoring here includes: - [x] Cleaning the code (removing unused...
Since the frequencies are calculated on the fly (`export` or `query` mode), I think it would be a nice feature to add new variants to an existing database, rather than...
When querying a database, would it be possible to add an option so the user can define the VCF header? Right now it always says: ``` ##INFO= ##INFO= ``` But...
Hi there, I merged four SV callers using svdb merge (delly, smoove, manta, tiddit). Then I tried running the merged VCF through vcfanno to annotate with genomic features and ran...