-
Hi dxCompiler team,
One of the scientists I work with is reporting an issue with one of her workflows in that an execution is not starting on DNAnexus even though all of its inputs are satisfied.
…
-
Hey all,
Just to give a disclaimer, I am most definitely VERY new to coding and bioinformatics and so it's quite likely I'm missing something simple!
I have posted this issue [here](https://github.c…
-
Hi,
I am a newbie using Annovar and just encountered this. I have annotated a vcf file, following the instructions. I have noticed that CADD_phred has dots for some variants and numbers for others.…
-
Hi,
We are using version bioconductor-purecn V 2.0.2 for our analysis of the selection of clonal mutations, recently we have tried V 2.4.0 and noticed that many mutations are filtered out specifica…
-
Dear authors,
While I was filtering a vcf to grab only its indels I noticed that the output also reports "indels" that are longer than 50 bp. Is this an expected behaviour? Shouldn't variants longe…
-
Running:
```
jba manta/manta.tumor.svs.hg38.vcf cov.rds --field ratio --purity 0.7 --outdir $PWD/jabba --name test --cores 8 --gurobi TRUE
```
The cov.rds file contains the column `ratio` whic…
-
Hi I have recently moved to using a new cluster. I am using version: ipyrad [v.0.9.95] on a cluster using 20 cores
ipyrad [v.0.9.95]
Interactive assembly and analysis of RAD-seq data
----…
-
# Combined Annotation Dependent Depletion (CADD)
- [ CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome. ](https…
-
### Data Owner Name
National Library of Medicine (NLM)
### What is your role related to the dataset
Data Preparer
### Data Owner Country/Region
United States
### Data Owner Industry
Life Scienc…
-
Hello Team,
I am trying to use PureCN with a matched tumor and normal samples, however, it's throwing an error. I am attaching the log file here. I have used CNVkit for segmentation and Mutect2 (G…