Annotate_rows between 2 different reference genome matrix tables

Hail Query & hailctl
1

Hello Hail team,

I have two different Matrix tables (MTs). The name of MTs are mt and allmt.
The reference genome of allmt is “GRCh37” and that of mt is “hs37d5” which is kind of GRCh37.
What I wanted to do is as below.


allmt = allmt.annotate_rows(MAF_tommo = mt.rows()[allmt.row_key].info.AF,
                           AC_tommo = mt.rows()[allmt.row_key].info.AC,
                           AN_tommo = mt.rows()[allmt.row_key].info.AN)

However, the code generated error messages as below.

-------------------------------------------------------------------------
TableIndexKeyError                        Traceback (most recent call last)
~/miniconda3/envs/hail/lib/python3.7/site-packages/hail/table.py in index(self, all_matches, *exprs)
   1777         try:
-> 1778             return self._index(*exprs, all_matches=all_matches)
   1779         except TableIndexKeyError as err:

~/miniconda3/envs/hail/lib/python3.7/site-packages/hail/table.py in _index(self, all_matches, *exprs)
   1848                     and isinstance(exprs[0], StructExpression)):
-> 1849                 return self._index(*exprs[0].values(), all_matches=all_matches)
   1850 

~/miniconda3/envs/hail/lib/python3.7/site-packages/hail/table.py in _index(self, all_matches, *exprs)
   1851             if not is_interval:
-> 1852                 raise TableIndexKeyError(self.key.dtype, exprs)
   1853 

TableIndexKeyError: 

During handling of the above exception, another exception occurred:

ExpressionException                       Traceback (most recent call last)
<ipython-input-49-3a9bf305d4d1> in <module>
----> 1 allmt = allmt.annotate_rows(MAF_tommo = mt.rows()[allmt.row_key].info.AF,
      2                            AC_tommo = mt.rows()[allmt.row_key].info.AC,
      3                            AN_tommo = mt.rows()[allmt.row_key].info.AN)

~/miniconda3/envs/hail/lib/python3.7/site-packages/hail/table.py in __getitem__(self, item)
    374 
    375         try:
--> 376             return self.index(*wrap_to_tuple(item))
    377         except TypeError as e:
    378             raise TypeError("Table.__getitem__: invalid index argument(s)\n"

~/miniconda3/envs/hail/lib/python3.7/site-packages/hail/table.py in index(self, all_matches, *exprs)
   1778             return self._index(*exprs, all_matches=all_matches)
   1779         except TableIndexKeyError as err:
-> 1780             raise ExpressionException(f"Key type mismatch: cannot index table with given expressions:\n"
   1781                                       f"  Table key:         {', '.join(str(t) for t in err.key_type.values()) or '<<<empty key>>>'}\n"
   1782                                       f"  Index Expressions: {', '.join(str(e.dtype) for e in err.index_expressions)}")

ExpressionException: Key type mismatch: cannot index table with given expressions:
  Table key:         locus<hs37d5>, array<str>
  Index Expressions: locus<GRCh37>, array<str>

I think this error is because of the different reference genome.
Could you let me know if there are some ways to solve this problem?

Thanks in advance.

2

I could solve this problem by importing VCF of “hs37d5" using reference_genome=‘GRCh37’ and skip_invalid_loci.