Releases: genid/Yleaf
Releases · genid/Yleaf
3.2.1
Yleaf v3.2
• Included support for vcf files
• Optimized the prediction algorithm by adapting the QC1 value to the Yfull tree
• Added the –cr option for CRAM files
• Added the –pq option to define the prediction quality threshold
• Increased the default –pq to 0.95 making the prediction more stringent
• Resolved compatibility issues when using the –old option
Yleaf v3.1
- Added an option to find private mutations.
- Added an option to draw a haplogroup tree showing the relation between samples.
- Simplified command line input. You now only have to provide what reference genome you are interested in and the rest of the files will be located automatically
- install.py is not used anymore. Instead files are downloaded the first time or you can use a config file to point to where you want Yleaf to look for reference genome data.
- Yleaf can now be called from anywhere after pip installing it.
Yleaf v3.0.1
Changes:
- A fix in the WGS_Yfull_hg19.txt position file that caused a crash.
- Minor bug fix that caused a missing value in the final prediction table.
- Some support for cross-platform use.
Yleaf v3.0
The new 3.0 version of Yleaf is out and ready. These are the most important changes that were made:
- Haplogroup relation tree is now based on YFull(v10.01) and ISOGG data. Not using the ISOGG marker identifiers anymore as a result.
- Tree has been updated with new information from both YFull(v10.01) and ISSOG.
- A haplogroup can now be ancestral, derived or undefined. This depends on the percentage of markers in that state. If more than 60% of markers are in ancestral or derived the haplogroup will the majority group. If the 60% threshold is not met the haplogroup is undefined and will not be taken into account for quality score calculations. This change affects the scores of QC1 and QC3.
- A script to convert ISOGG marker tables into a format usable by Yleaf. These tables can unfortunately only be used together with the -old flag.
Yleaf v2.2
readme release v2.2