grenedalf

This is the first release since the grenedalf manuscript came out 🥳

grenedalf: population genetic statistics for the next generation of pool sequencing.
Lucas Czech, Jeffrey P. Spence, Moisés Expósito-Alonso.
Bioinformatics, 2024. doi:10.1093/bioinformatics/btae508

Notable Changes

• Fix window averaging option check segfault #31
• Refine pool sizes documentation #16

This release adds some features related to position masking. Furthermore, it renames a few options for consistency: Options that ended in -file are now more concisely named.

Notable Changes

• Add window averaging with a provided mask #24
• Add per-sample mask options #25
• Add --make-gapless option #26
• Add bed mask invert option
• Add option to set missing value for frequency table
• Rename -file option names for clarity
• Use a faster thread pool for speed gains with few samples

Bug Fixes

• Fix missing data treatment in window average available loci setting #26
• Fix ref base lower case comparison issue

Notable Changes

• Minor fix of SVG axis boundaries issue #23

Notable Changes

• Minor fix when reading VCF with indels and AD data, #21
• Add numerical filters and subsampling to sync command

This release fixes the wrong computation of FST window averages that slipped our attention in grenedalf v0.4.0, and adds tests to avoid these types of accidents in the future. Other than that, please see v0.4.0 for the major updates of this version compared to the previous v0.3.0.

Notable Changes

• Fix broken FST window normalization
• Add independent implementation test
• Add example files

This release contains a major redesign of the data filtering approach, which now allows to properly compute window averages of the statistics, and improves the behavior of the SNP queue window approach. It furthermore contains several refinements of the statistics, and offers more options than before. Some options have been renamed to fit with the new functionality.

ATTENTION: We accidentally introduced a bug in the window averaging of FST that slipped our attention. We are currently working on a fix, which will be released asap. Please use fst --window-average-policy absolute-sum in the meantime only.

Notable Changes

• Add several window averaging policies for statistics
• Add refined Tajima's D denominator policies
• Add fst cathedral plot commands
• Refine sync command with gsync, header, and masked annotation
• Add sample group merging option
• Add options to provide a genome mask file
• Add re-scaling and re-sampling functions for samples
• Rename sliding window option into interval window
• Rename "coverage" to "read depth" throughout the documentation
• Add more general documentation

Notable Changes

• Add and refine numerical filter options
• Refine handling of positions with deletions and add respective options
• Refine handling of multiallelic positions, e.g., for VCF input and Karlsson Fst
• Streamline and simplify sample naming in name filters and output files
• Accept sync files with sample name headers and missing data annotation
• Add optional output of intermediate Pi values to fst command

Preprint

This release accompanies our preprint

grenedalf: population genetic statistics for the next generation of pool sequencing.
Lucas Czech, Jeffrey P. Spence, Moisés Expósito-Alonso.
arXiv, 2023. arXiv:2306.11622

grenedalf is still very much in development, and a lot of things will further change, such as the command structure and option names. We are lacking documentation, and there are some known smaller issues. That will all be fixed in the near future. However, since its initial pre-release more than a year ago, a lot has changed and improved. We hence consider it workable enough. But still, please report any issues that you are having - grateful for your feedback!

Stay tuned for more!

Notable changes

A lot has happened since v0.1.0, but here is a very broad summary:

• Add our novel asymptotically unbiased FST estimators
• Add support for multiple file input, with union or intersection
• Add support for generic frequency table files
• Add different windowing approaches (regions, whole genome, etc)
• Add a plethora of convenience options for filtering and subsetting
• Add region filters (bed, gff, and other region file formats supported)
• Rename, refine, and reorganize commands and options
• Fix a lot of early teething troubles (setup, threading, minor bugs, etc)

This (pre-)release is meant for those who have (thankfully) been working with grenedalf already, as a point of reference.

It is not to be considered stable - things WILL change!