cannot complete a validation run

[MattWellie]

Relevant working batch
https://batch.hail.populationgenomics.org.au/batches/110146

The command which previously ran to completion and generated results isn't currently working

We have updated the container used to a much more up-to-date version of hap.py, but running using the old image also failed

Issue created Illumina/hap.py#163

Nature of issue:
the hap.py preprocessing step seems to be wrongly processing indels, taking them out of order. The false ordering then causes the indexing step to fail.

Pre.py is mostly a bcftools call-chain, which works fine for me locally on v1.13.1

The BCFtools version in the hap.py github is 1.4.1 (2017) and the current is 1.15.1, so I'm attempting a rebuild with updated HTSlib adn BCFtools, to see if this resolves.

If not, deactivating all pre-processing steps could be a solution, but feels like a huge compromise (not sure if it's entirely possible)

[MattWellie]

This was resolved by using an updated version of BCFtools (see populationgenomics/images#37)