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eldariont
Structural Variant Identification Method using Long Reads
Hello. We have generated several PacBio data. As I understand it, svim calls SV for each sample. Can it process multiple samples together? My current idea is to call SV...
Hello! I was wondering if the start and end positions reported in the VCF are 0-based or 1-based. Best regards, Jonatan
# Bug description Running SVIM on some long read PacBio bam files, I get an error from tabix, that the resulting sequences are unsorted. ```bash [E::hts_idx_push] Unsorted positions on sequence...
Hi, I'm using your excellent work (SVIM) to carry out some evaluation. And I found that in your supplementary data: ``` Under https://www.molgen.mpg.de/~svim/svim_evaluation.zip, we provide a compressed directory with the...
Hi, I encountered problems with SV naming of DUPs (DUP:INT and DUP:TANDEM) when I wanted to merge output VCF files from SVIM with a merging software (Jasmine). Having a semi...
Hello! I've noticed on running `svim alignment` that despite providing the reference that the reads were aligned to, all the reference alleles in the output VCF file are `N`. Is...
Hello! Are there any plans on uploading the v2.0.0 of svim to conda to make it easier to implement in pipelines? As of now the latest version available in conda...
Hello! I think it'd be a good thing to implement the ability to specify the name or at least a prefix of the output file, in case multiple files are...
hello! using svim alignment to genotype, all the tandem duplications show missing value. 1. generated simulated data by VISOR LASeR, here is my input: 1 122200 125000 tandem duplication 2...
Hi, SVIM is a good SV caller and can be implemented easily. Could I run it with multithreading and how to do like this? Hope your reply. Thank you!
