@tpoterba how would one run something similar but when AF isn’t defined for every entry:
I tried:
chip_vars_mt = chip_vars_mt.annotate_cols(test =
hl.agg.filter(hl.is_defined(chip_vars_mt.AF), hl.agg.mean(chip_vars_mt.AF[1])))
chip_vars_mt.col.test.show(1)
But get the following error:
Hail version: 0.2.34-914bd8a10ca2
Error summary: HailException: array index out of bounds: index=1, length=1
----------
Python traceback:
File "<ipython-input-131-84c67a4862a4>", line 2, in <module>
hl.agg.filter(hl.is_defined(chip_vars_mt.AF), hl.agg.mean(chip_vars_mt.AF[1])))
Thoughts?