Announcing PHGv2.4

[zrm22]

We are pleased to announce the release of PHG version 2.4.

The main improvements of this version are to update some of the dependencies of the PHG.

In this version, we have updated both AnchorWave and AGC to their most recent versions.

AnchorWave has been updated to version 1.2.3, which changes the assembly coordinates for negative stranded alignments reported in the MAF file. This means that if you process a MAF file generated from a previous version of AnchorWave using phg create-maf-vcf with default parameters, the corresponding gVCF file will have incorrect coordinates. To remedy this, we have added a --legacy-maf-file option to handle old MAF files. Please refer to the documentation for more information.

AGC is also updated to version 3.1. This may cause some errors when trying to retrieve sequences. To remedy this you may need to delete your existing conda environment and then rerun the phg setup-environment command.

Please let us know on the Github Issues page if you encounter any problems.