Christoffer Flensburg

Hi! Ok, so we are finally back to the original problem! 🎉 I will keep an eye out for the featureCounts issue in R 4.0.0+ though... If you can you...

Hi, sorry I dropped the ball on this one. Is this issue still relevant? Essentially you load the `allVariants.Rdata` into R, located in the R directory of the individual, and...

Hi Justin, Yeah that is an issue with a few overlapping genes. I am no longer running VEP in superFreq, because it was causing dependency issues for a large number...

It means 27 copies of A and one copy of B, so a short for AAAAAAAAAAAAAAAAAAAAAAAAAB (if I got that right). I realise now it's ambiguous, but not sure how...

Yeah it does happen that you get hundreds of copies of oncogenes sometimes. It probably happens more often that QC issues give you false calls though. :P The read counts...

If you have 10-20x coverage across the entire genome with extra bumps over the exons, then it seems like you've got sequencing data from both a genome and an exome....

I think exome default is 0.02, RNA-Seq default is 0.1. So I think up to 0.1 is fine and you should still have decent sensitivity. If a lot of noise,...

Plot directory, data subdirectory, the files with "segment" have the segment information. "call" column has the genotype, so AB for normal two copies heterozygous, A for loss, AAB for gain,...

Hi Sohyoung, I am not sure what caused that error. I'd need the log file to understand better. Alternatively, as this seems to be a difference between version, I am...

hey! The reported reference NNNN in deletions is a known issue that I probably won't fix soon. Essentially I set things up in a stupid way only accounting for SNVs,...