Comments (2)
Make sure running start to finish includes VEP and slivar in $PATH or are contained in the program?
from bayescmg.
the run.sh bAyesCMG script now checks that vep is installed. Slivar is automatically downloaded when bAyesCMG is gotten from git.
from bayescmg.
Related Issues (15)
- Write scripts for parsing on PostP and other useful things HOT 1
- Make sure BP7 is VEP Consequence is synonymous and NOT splice_region and check counting the number of synonymous variants HOT 1
- Processing on unannotated vcf in new environment HOT 2
- run.sh crashes even with all necessary components in PATH HOT 3
- Rename everything VaBayes to bAyesCMG HOT 1
- Fix run.sh message HOT 1
- run.sh should not download clinvar and other data to current directory HOT 3
- Add variant quality filtering using slivar
- Check variant logic being only applied to variants present in proband
- Skip (pre) processing steps if possible
- Add a flag to keep intermediate files or not HOT 1
- VQSRTranche variants being retained HOT 1
- Need to annotate VCF before slivar comp het function HOT 1
- Getting multiple clinvar tbis HOT 1
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