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Population-scale genomics
The current VCF spec version is [4.3](http://samtools.github.io/hts-specs/VCFv4.3.pdf). The VCF we're outputting is marked as 4.2. Check if there's anything new in the spec that contradicts current usage, and update the...
Follow up to #2445. The default sample names in our VCF mapping are always ``tsk_0``, ``tsk_1`` etc, and these may not have anything to do with the IDs of the...
We are currently using the ``tree_sequence`` attribute of a way of determining whether a variant is a frozen copy or not. We also use the ``variant->site.position`` attribute as a way...
Here's a draft of the C code to compute covariances of aribtrary weighted sums of genotypes. Borrowing from @brieuclehmann's code, this should always be true: ``` def genetic_relatedness_matrix(ts, sample_sets, mode):...
In #2439 we added the MetadataTable as the superclass of tables that have a metadata column. However, much of the functionality around dealing with things that do/don't have metadata is...
See #2127. See also #1190 for when keep_unary_in_individuals was added. This is a quick prototype to show how it can be done. Essentially we just need to make a second...
We currently don't have any simple C example code for decoding variants. This is useful both for C API users and ourselves for timing/bug tracking purposes. This is roughly what...
Imputation quality score (IQS) is another popular way to measure genotype imputation performance (discussed in #2193). This paper proposed IQS (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2837741/). IQS accounts for chance agreement, whereas overall concordance does...
As part of https://github.com/tskit-dev/tutorials/issues/182 we should think of alternative ways of showing big trees. One possibility is to collapse clades in a tree if e.g. all the nodes underneath belong...
