Serhiy Naumenko

Thanks @brentp ! This binary works. However, even with -permissive-overlap option on, annotation happens only when POS in the query is the same as POS in the GNOMAD. When I...

Thanks @brentp! I've got it - when working with intervals, it is better to annotate a vcf file vs bed file rather than vs vcf. Still I have some minor...

Hi @brentp ! I see two issues. In both annotation happens. One issue is incorrect annotation, another is too permissive annotation (better to have no annotation there). To reproduce both...

Hello everyone! I was lucky to install with: 1. Install development version of R4.0 (not sure if that helps installing velocyto.R, but I needed it because one of the packages...

Hello everyone! Disclaimer: I'm not a part of **velocyto-team** See above I was able to install on Rdev. Now I installed on a Desktop Fedora 30 5.2.9-200.fc30.x86_64 with the latest...

Hi! How did you load information to GEMINI.db? First query works for me: ``` gemini query -q "select synonym from gene_summary where gene='ARTEMIS'" NA12878-1-ensemble.db A-SCID,FLJ11360,SNM1C,DCLRE1C,SCIDA A-SCID,FLJ11360,SNM1C,DCLRE1C,SCIDA ``` For the second...

Yes, I modified the root_path, so the script picks up the file. Thanks, this new report looks nice for me. Actually I have 12 samples and I need to do...

Hi again! Now I have all the samples and I'm working with the report [https://github.com/lpantano/seqcluster/blob/master/seqcluster/templates/report.rmd](https://github.com/lpantano/seqcluster/blob/master/seqcluster/templates/report.rmd) First, I've changed ``` #metadata = read.csv(metadata_fn, row.names="sample_id") metadata = read.csv(metadata_fn) metadata = metadata[,1] #sample_ids...

Ok, I'll update and restart. About the dataframe ``` group HI_3550_004_RPI1_R4215_R1 fake HI_3550_004_RPI3_R4217_R1 fake HI_3550_004_RPI5_R4219_R1 fake HI_3550_005_RPI41_R4228_R1 fake HI_3550_005_RPI43_R4230_R1 fake HI_3550_005_RPI7_R4226_R1 fake HI_3550_004_RPI2_R4216_R1 fake HI_3550_004_RPI4_R4218_R1 fake HI_3550_004_RPI6_R4220_R1 fake HI_3550_005_RPI42_R4229_R1 fake...

Line 38, it is just reading of summary.csv - samples list ``` metadata_fn = list.files(file.path(root_path), pattern = "summary.csv$",recursive = T, full.names = T) metadata = read.csv(metadata_fn, row.names="sample_id") condition = names(metadata)[1]...