Edoardo Giacopuzzi

details of merge options

13

Hi, I want to use SURVIVOR merge to merge calls from several VCFs. I've downloaded the latest release version and the help message for merge command reports these 2 options...

better explanation of graphtyper output VCF

2

Hello, Can you please provide some more details on the format of graphtyper output VCF? I'm interested essentially in 2 points: 1. Variants definitions. Take the following example: Given my...

Cellranger module

4

Hello MultiQC team, I've created a new module to integrate cellranger QC metrics from VDJ or count analysis into MultiQC reports - [x] `CHANGELOG.md` has been updated - [X] There...

Get list of INFO and FORMAT keys from Header

1

Hi Brent, Is there a way to get the list of keys for INFO and FORMAT definitions from the header of a VCF using hts-nim? The idea I'm working on...

Select subset of INFO tags

2

Hi, I'm wondering if there is a method to select only a subset of INFO tags when reading a variant. What I want to achieve is reading a VCF and...

Run stand-alone hiPHIVE prioritization

3

Hi, I'm wondering if it is possible to run the hiPHIVE prioritization as a stand-alone tool providing a list of HPO terms. Basically, I want to get a list of...

Installing and running glow outside of databricks

10

Hi, My setup is Spark v3.1.3 with Hadoop v3.2.2 and PySpark v3.1.2 and latest glow.py. I'm trying to read some BGEN files into GLOW from my a jupyter notebook. I...

somalier ancestry and relate freeze on writing output on BeeGFS filesystem

5

Hi Brent, I'm setting up a pipeline which includes somalier for QC and I'm experiencing a strange behaviour. Essentially, the pipeline is managed by Nextflow and I place the work...

Hi, I'm trying to use velocyto.py to analyze single cell data. If I run it interactively all works fine, but I'm having a strange issue when submitting to HPC using...

Hi, I'm trying to use svtools classify as suggested in Classifier.md After following all the steps in your tutorial I've successfully generated a VCF with SV calls for ~85 samples....