Released October 20th 2014
#####Features:
- Identification of SV breakpoints.
- Identification of soft-clipped consensus.
- Provides the end of breakpoints using supplement alignments.
- Provides genotypes and genotype likelihoods for multiple individuals.
- Multi-threading enabled, supported by OpenMP.
#####Known Issues:
- For large population calling WHAM can hit the Ulimit.
- For deep regions WHAM has considerable slowdown.
- Memory becomes an issue for deep regions.
#####Future efforts:
- Improvements to speed and memory usage.
- Improve WHAM's break-point joining.
- Improve the LRT for association testing.
Released October 24th 2014
#####Features:
- WHAM now only reports SVs where the consensus is longer than 10bp.
- WHAM can now be built in debug mode, which prints all critical data structures
make debug
#####Known Issues: Same as Version 1.0.0
#####Future efforts: Same as Version 1.0.0
#####Bug fixes:
- Now using discordant mate-pairs correctly.
- Major improvements to accuracy on simulated data
- More SVs have paired breakpoints
Released October 31th 2014 - happy Halloween!
#####Features:
- Increased overall accuracy of SV calls
- Added attributes to VCF file for SV type classification
- Added utils/classifier_parse.py for SV classification
- Added functionality to readPileUp Class
#####Known Issues: Same as Version 1.1.0
#####Future efforts: Same as Version 1.1.0
#####Bug fixes:
Released Nov 4th - happy voting!
#####Features:
- Increased overall accuracy of SV calls. Large calls and translocations require more support.
- Added another attribute for the classifier.
#####Future efforts:
- Validation on published data sets.
#####Bug fixes:
Released Nov 12th - happy Veterans Day -1
- Added deltaAfWham for pooled sequencing experiments.
- Classifier now prints cross-validation information.
#####Future efforts:
- Adding subsampling to the genotype model.
#####Bug fixes:
- High depths were causing the genotype likelihood model to underflow. This is fixed. Only the first 1k reads are considered for a genotype call.
- Fixes to the VCF header again
Released Nov 17th
- A pileup bug was resulting in bad genotype calls.
#####Future efforts:
Futher efforts to improve genotyping.
Released Nov 30th
- Added mate-pair end-point clustering.
- Several INFO and GENOTYPE fields were changed.
None
#####Future efforts:
More benchmarking.
- Added average mapping quality (MQ)
- Fraction of reads with quality lower than 50
- Filtering out reads with mapping quality below 40 (better specificity)
- Set several cutoffs based on CHM1 data
None.