andrewSharo

Set minimum width for flow

2

Fantastic work on this tool! I have found it very helpful and plan to cite it in an upcoming publication. I have one quick question. I believe there was a...

Best FORMAT field for filtering SVTyper Output

2

Hi Dave, I'm running SVTyper on output from Lumpy for hg38 whole genome samples with 50x depth, interested in finding Deletions and other SVs with a low false-positive rate. The...

Dear Selene Developers, Thanks for creating Selene. I'm finding it super helpful for getting into CNNs. I have trained a model with 36 features using Selene, and this model is...

Hi Brent and Dave, Not sure if this question is more appropriate here or under svtools. I have been jointly calling SVs in families with Lumpy. Is there a command...

PE=0 for all SVs derived from 10X Long Ranger bams.

3

Hi Ryan, I'm running lumpy v0.2.13 because I need to compare to some earlier analysis. When I run lumpyexpress, it outputs a vcf where all records have 0 PE support....

I have a vcf full of SVs, and I want to read them in as class vcf.model._Breakend instead of vcf.model._Record. Then I can easily query their connectingSequence and other variables....