Ag3 discordant read calls version 20250214

A new discordant read calls version 20250214 has been released for the Ag3 data resource. This is now the default discordant read calls version when using the malariagen_data Ag3 API. This version is available for datasets up to and including Ag3.14.

To pin this cohorts analysis when accessing data:

import malariagen_data

ag3 = malariagen_data.Ag3(
    discordant_read_calls_analysis="20250214",
)

This new version introduces some key changes:

• An error in the underlying data describing absence or presence of CNV alleles has been corrected for samples that were not called for CNVs.
  • All samples in the Ag3 resource that are classified as intermediate_gambcolu_arabiensis on the aim_species field have been updated from presence 1 to absence 0, as these intermediate samples are currently excluded from CNV calling.

If you need to access the previous version of the discordant read calls, you can pin it by using 20230911 as the version in the discordant_read_calls_analysis parameter when calling the malariagen_data API, as described on the code snippet above.