# Filter for specific variants

**URL:** <https://discuss.hail.is/t/filter-for-specific-variants/3503>\
**Category:** Hail Query & hailctl\
**Created:** [July 21, 2023, 9:09pm UTC](https://discuss.hail.is/t/filter-for-specific-variants/3503 "2023-07-21T21:09:57Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![anh151](https://avatars.discourse-cdn.com/v4/letter/a/ce73a5/32.png) [@anh151](https://discuss.hail.is/u/anh151)\
**Post date:** [July 21, 2023, 9:09pm UTC](https://discuss.hail.is/t/filter-for-specific-variants/3503/1 "2023-07-21T21:09:57Z")

</div>

Hello,  
Lets say I have a small MatrixTable (~1000 variants) that has multiallelic variants that have been split. I only want certain variants. For the example shown below I would only want the variant that is A-\>G. I have a dataframe which contains the chromosome, position, ref and alt bases that I want. I know I need to use `filter_rows`, but I’m struggling with building the filter expression.

```python
chr1 1000 A G
chr1 1000 A T

```

```python
# variants are set up as chr1:1000:A:G
ht = hl.Table.from_pandas(variants)
ht = ht.key_by(**hl.parse_variant(ht.variant))

```

```python
#Attempt 1
mt_filtered = mt.filter_rows(ht[mt.locus] & ht[mt.allele])

---------------------------------------------------------------------------
TableIndexKeyError Traceback (most recent call last)
/opt/conda/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:

/opt/conda/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)
/tmp/ipykernel_238/3591338782.py in <module>
----> 1 mt_pgx_only = mt_combined_cleaned.filter_rows(ht[mt_combined_cleaned.locus] & ht[mt_combined_cleaned.allele])

/opt/conda/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"

/opt/conda/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<GRCh38>, array<str>
  Index Expressions: locus<GRCh38>

```

```python
#Attempt 2
mt_filtered = mt.filter_rows(ht.locus[mt.locus] & ht.alleles[mt.allele])
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
/tmp/ipykernel_238/483111301.py in <module>
----> 1 mt_pgx_only = mt_combined_cleaned.filter_rows(ht.locus[mt_combined_cleaned.locus] & ht.alleles[mt_combined_cleaned.allele])

TypeError: 'LocusExpression' object is not subscriptable

```

---

<div class="post-metadata">

**Author:** ![anh151](https://avatars.discourse-cdn.com/v4/letter/a/ce73a5/32.png) [@anh151](https://discuss.hail.is/u/anh151)\
**Post date:** [July 23, 2023, 7:46pm UTC](https://discuss.hail.is/t/filter-for-specific-variants/3503/2 "2023-07-23T19:46:02Z")

</div>

Finally got it.

```python
# variants are set up as chr1:1000:A:G
ht = hl.Table.from_pandas(variants)
ht = ht.key_by(**hl.parse_variant(ht.variant))

mt_filtered = mt.filter_rows(hl.is_defined(ht[mt.row_key]))

```