Anne Marie Noronha

i actually think better curation of the entire Immgen data set may be helpful. For example, there exists: > Epithelial cells | Epithelial cells (Ep.5wk.MEC.Sca1+) > Epithelial cells | Epithelial...

i found at least one of the offending lines: ``` ##FILTER= ``` `vcftobedpe` turns this line into: ``` ##FILTER="> ``` and then this line becomes unparseable with with `bedpetovcf`. i...

i also encountered this error with 0.5.1, and as a temporary workaround i just filtered out calls with no END. but this is not ideal and it might be necessary...

i seem to have installed svtools using #300, but instead of `statsmodels==0.90` (couldn't be found in PyPI) I used `statsmodels==0.11.0` (that's the version included in `docker://halllab/svtools`). However, the svtools does...

Looking forward to this as well. I am interested in knowing the definitions of each column in the `_germline` and `_somatic` files (is `difference` just the difference of the mean...

here's a related example. we have two vcfs that are both called by SvABA on the same sample but vcf A was run by us and vcf B was called...

well i think i figured it out. SURVIVOR does not like the GT field, but this is (somewhat) remedied by specifying minimum caller to be 0 instead of 1. Then...

I am using version AnnotSV 3.0.9, so perhaps not the absolute latest one but still pretty recent. i repeated with 3.1 and got results that matched your output. The webportal...

We have UMI in bulk RNA-seq, not scRNAseq. i guess we went for vanilla kallisto first because bustools seemed to be specifically for scRNAseq with cell and molecular barcodes, but...

oh ok, so it looks like we don't need an R3 read file in that case, if i'm reading that right, which is great! i think we would prefer the...