Grant Neilson

icon company Cosyne Therapeutics

Results 7 comments of Grant Neilson

Error with Pandas 2.0.0

I have also come across this issue

Per gene copy number signal.

Hi I am working on PR and adding to #58 that will allow you to extract the per gene copy number by averaging across all the bins a given gene...

VCF2MAF and allele frequency

Hi @berguner I have been using the Nextflow pipeline here (dev branch) https://github.com/FriederikeHanssen/vcftomaf/tree/dev To do the conversion it automatically includes all VEP annotations present in the info column

CNVkit reference issue for WGS tumor-only samples

Hi, I am also experiencing this issue, how did you end up creating your reference @berguner?

CNVkit reference issue for WGS tumor-only samples

Hi @berguner to build the reference using on the `batch` command you need to either A) provide a tumor bam/cram and normal bam/cram or b) just a normal bam/cram i.e...

CNVkit reference issue for WGS tumor-only samples

Hi @FriederikeHanssen I will look at it, can you please link the PR?

CNVkit reference issue for WGS tumor-only samples

> Yeah, users should provide a reference created from a pool of protocol-matched normal samples when they don't have matched normal samples. I would even say that we should enforce...