Fixes to Consensus Calling and Updated Depth Calculation #5
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added 30 commits
September 19, 2024 00:23
- Added script fo filter incompataible variants from VCF file - Modified consensus calling scripts to use this filtering
Fixed Bug where TRACESPipe tried to save incorrectly named VCF Restructured VCF naming during consensus calling
alignments and cut off peaks at 1000
Also modified handling of sensitivity to reduce duplication of code Added git ignore for swp files
These changes moved to a branch This reverts commit 8d962be.
Changed VDB.fa in code to a variable for future maintainability
all branches of TRACESPipe (will use updated depth calcs)
virus REFTYPE swapped with viral
depth calculation no longer inverted
This effectively converts all depth and breadth calculations to the
non-supp/sec+maxDepth method
Fixed typos/language in some comments
Merging commits up from master
Update to match parent branch
added 12 commits
June 12, 2025 16:47
Bring up typo fixed made in parent
Internal Viral Names System file created to track default supported viruses Viral Names in src dir now contains the set of viruses used in the analysis Removed all hardcoded viral lists
Removed blank line from internal viral names which leads to a fatal check for empty virus filtering scripts
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The following changes have been tested on two analysis runs.
Fixed a bug where called variants which are incompatible (eg. overlapping indel and snp) would lead to truncated consensus sequences.
The Bug was fixed by introducing a step where such incompatible variants are filtered out.
As samtools mileup is now no longer supported, consensus calling has been updated to use bcftools mpileup.
Depth of coverage calculation has been updated to use samtools bedcov, this allows ignoring excessively covered regions and automatically ignores secondary and supplementary reads which artificially inflate the depth.
Made a few changes to streamline and generalize code: