Comments (1)
Hi @rescuz
I believe that was a typo in the runDemo.sh file. I apologize for that.
If you look at the actual charger command that the script is running, you will see it does not take the pathogenicVariants.vcf file into account.
If you do want to use a similar file in your analysis, there is an example vcf for pathogenic variants in the PanCanAtlasData directory (PanCanAtlasData/emptyRemoved_20160428_pathogenic_variants_HGVSg_VEP.vcf.gz).
This file was used as a CharGer input in our Pan-Cancer germline study (https://doi.org/10.1016/j.cell.2018.03.039). Just make sure to decompress it before use.
Hope this helps
Fernanda
from charger.
Related Issues (20)
- All variants classified as Benign or Uncertain Significance HOT 4
- something wrong HOT 7
- run demo.sh, report error HOT 2
- can you give me an example command with run VEP? HOT 4
- I can not get any output file using v0.6.0b1 version HOT 1
- Problems to run CharGer v0.5.4 HOT 5
- IndexError: list index out of range while running with Mac-Clinvar HOT 4
- Provide instructions to generate the HotSpot3D cluster file
- Null Variant classified as Benign HOT 3
- installed Charger 0.5.4 but version in help is 0.5.3 HOT 1
- error: Hint: is the input amino acid change column correct , charger version 0.5.4 HOT 1
- Reference for inheritanceGeneList 20160301_Rahman_KJ_KH_gene_table_CharGer.txt.gz HOT 2
- What Cross-reference data files to use and where to get for lung cancer
- CharGer::runIndelModules Error:
- Install error
- NameError: global name 'entrezaip' is not defined when doing clinvar search
- is this software alive?
- Need most updated ClinVar files
- PM5 found 0 pathogenic variants
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