-
Hi,
I noticed that the pipeline detects some somatic mutations with VAF = 1 in a specific cell type. Such mutations may be an example of cell-type-specific clonal expansion which may not be true so…
-
In germline mode, there is no DR or DV field in the sample information, while the description of them occurred in the comment part
```plaintext
chr6 32648276 7184 N CSV . PASS END=32652372;SVLEN=4…
-
Hi @kcleal
What would be the best practice to estimate Structural Variant Allele Frequency for outputs generated from the Dysgu tool on a cohort of 300 samples? Currently, I'm trying to use `bcfto…
-
I am using --vaf 5 --maf 0.001 --minDepth 50 --minAltDepth 2, but its throwing an error like "Warning : given vaf >> vaf in config. wrong vaf threshold ?". if i set --vaf 1 or less then 1 then its wor…
-
v
-
**Describe the bug**
vaf/vif not working in Lua code
**To Reproduce**
1. install nvim-treesitter and nvim-treesitter-textobjects
2. load a .lua file
3. move cursor inside a Lua function definit…
-
--Hi,
how to set Vardict to detect variants with VAF ~ 1%, which parameters can increase sensitivity ?
than you --
-
Hi,
I have a VCF that was processed with [HiPhase](https://github.com/PacificBiosciences/HiPhase). The file contains lines with "|" as well as "/" for the `GT` value. Example:
```
chrX 1189233 …
rollf updated
1 month ago
-
Hey,
thanks for the great simulation tool! We simulated reads using this command:
```bash
conda activate SWAMPy
python simulate_metagenome.py \
--genomes_file ../example/viralref.fasta \…
-
Hi,
Thanks for developing this nice tool.
I have two genomes, assembly1 and assembly2. My goal is to use these two genomes as reference genomes, align reads to each of them, and call variants. T…