sveval

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I would like to compare SV calls between two different methodologies, for example between a graph-based method and one which uses only a single linear reference. Is it reasonable to...

peterdfields

installation issues

1

Hi, I keep getting the following error when trying to install the package. Could you help me with this please? Best Wishes Kerstin ``` > BiocManager::install('jmonlong/sveval') 'getOption("repos")' replaces Bioconductor standard...

kerstinth

names attribute must be the same length as the vector

1

I get quite far into the pipeline before crashing now. But I still crash during the running of an sveval step. (on /private/groups/patenlab/rrounthw/sveval/snakemake in mustard) ``` I have no name!@9bf86e5c67f5:/app$...

Robin-Rounthwaite

Could sveval be less strict on variation in insertion/ref calls

4

If I have I compare a 0/1 insertion of `TTTTTT` with 0/1 `TTTTTTA` sveval will call it a match because the sequences are almost the same. But if I have...

glennhickey

Right now there is a parameter to define regions to run the evaluation on. Basically the overlap are computed and then the SVs are filtered to keep only the ones...

jmonlong

``` library(sveval) merged_vcf

Plogeur

Dear Jean, Thanks for creating this tool! Sadly, I'm struggling installing it. It seems that tidyr is now differently compiled (I get a cpp11-related error). I'm using the dockerfile from...

phpeters

We encountered the following error during the computation using the script. Could you help identify the possible cause? svs = lapply(list.files('pan_svs/', '.rds'), function(fn){ gr = readRDS(paste0('pan_svs/', fn)) gr$sample = gsub('(.)\.decomposed.svs.rds',...

C-YONG