gevro issues

Results 48 issues of


                                            gevro

setdiff not behaving as expected

Hi, For some reason the below setdiff is not filtering out the element in x, even though it is encompassed by y. x: ``` > mutations.gr[[1]][2] GRanges object with 1...

New long-read population reference

Hi, A new 1000- individual population long-read reference was just released for PacBio https://www.pacb.com/press_releases/pacbio-and-international-research-consortium-colors-announce-release-of-first-ever-hifi-long-read-variant-database/ It is here: https://zenodo.org/records/11511513 Specifically this file: CoLoRSdb.GRCh38.v1.0.0.pbsv.jasmine.vcf.gz Are you able to add it to AnnotSV?...

new annotation requested

Memory requirements

Hi, MuSiC is crashing with a single-cell reference of ~120k cells and 36 bulk samples due to memory limitations, even with 128 Gb RAM. What are the memory requirements? Thanks

Bwameth vs bismark

Hi, I'm curious if you have recommendations on which aligner/process is best to use in specific situations? Or is it purely just use user preference?

enhancement

good first issue

pbmerge - overlapping movie/zmw combination

Using the latest versions of Lima and pbmerge, I'm trying to re-merge samples that were demultiplexed by Lima. But pbmerge is throwing an error that there are overlapping movies/ZMW combinations....

sawfish

Hello, I just saw the pre-print on the new PacBio SV caller 'sawfish'. Will this be incorporated into the pipeline, and if so, what would the ETA be?

enhancement

vcf errors

Hi, The final vcf is giving me these errors when I look at it with bcftools: [W::bcf_hrec_check] Invalid tag name: "'SampleID'" [W::bcf_hrec_check] Invalid tag name: "Compound_htz(sample)" [W::bcf_hrec_check] Invalid tag name:...

bug

VariantConvert

gevro