Comments (3)
dillonl
commented on July 28, 2024
This is now done the way you suggested. clinvar data is now downloaded to the bAyesCMG install dir.
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mvelinder
commented on July 28, 2024
Still getting a data/ dir in the dir I'm running in
(base) [u0691312@redwood5:A569]$ ll data/
total 1075124
drwxrws--x+ 2 u0691312 marth 4096 Apr 20 11:40 ./
drwxrws--x+ 3 u0691312 marth 4096 Apr 20 11:40 ../
-rw-rw----+ 1 u0691312 marth 26624885 Apr 20 11:41 clinvar.grc37.vcf.gz
-rw-rw----+ 1 u0691312 marth 285247 Apr 20 11:41 clinvar.grc37.vcf.gz.tbi
-rw-rw----+ 1 u0691312 marth 1073999449 Apr 20 11:54 clinvar.grc37.vep.vcf
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mvelinder
commented on July 28, 2024
Working now
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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
- Update github documentation and README 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
- 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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