AnnotSV
AnnotSV copied to clipboard
lgmgeo
Annotation and Ranking of Structural Variation
Hi, When I use AnnotSV to annotate my SV file from Lumpy, I find the start positions were changed in the AnnotSV result. For example, `chr7:73743401-116381161` is the vcf file,...
i am testing annotsv and finding that the first few columns in certain examples do not make sense and I was hoping it could be clarified. i have the following...
Hello Veronique, Hope you are doing great. In annotations, I have noted that certain P_loss_coordinates are coming from Hg19 reference coordinates, despite I have provided the Hg38 mode in the...
Hi, For `omim database`, is it possible to get the `Omim Genes Symbol` column, `OMIM_ID /OMIM_phenotype / OMIM_inheritance / OMIM_morbid / OMIM_morbid_candidate` are already in the headers. For `ClinGene data`,...
If I'm using a vcf as my -SVinputFile, but want to use -snvIndelFiles, would I just use the same vcf for both inputs?
I am executing AnnotSV 3.0.5 and encountering this error frequently  If I re run the same command, it gets executed without any issue. Any ideas ?
Hello, I'm trying to generate HVGSg notation from some structural variants and translating them into HGVSc but for this I need the transcripts with the corresponding version, meaning the number...
Hi, Are you interested in reannotating SV_type column with `inversion/deletion/duplication/insertion`, not just `BND`? https://github.com/walaj/svaba/issues/4 Best, xiucz
Hello, I'm running AnnotSV for annotation of my dataset. After updating GenCC's gencc-submissions.tsv file from https://search.thegencc.org/download/action/submissions-export-tsv, i'm getting following errors: ``` ...listing arguments ****************************************** AnnotSV has been run with these...
from [share/tcl/AnnotSV/AnnotSV-write.tcl](https://github.com/lgmgeo/AnnotSV/blob/7973cc4725f548cac3f9cd2dc843ed47c5b3f1e0/share/tcl/AnnotSV/AnnotSV-write.tcl#L26), implement `OrganizeAnnotation` for pyAnnotSV. Breaking this into smaller issues would probably be a good idea. - [ ] created validation tests against AnnotSV output - [ ] validation...
