INNER JOIN (SELECT iq1.cohort_definition_id, iq1.concept_id, Sum(iq1.count_value)
                   FROM   (
                     SELECT cohort_definition_id,
                            CAST(CASE WHEN isNumeric(stratum_1) = 1 THEN stratum_1 ELSE null END AS INT) AS concept_id,
                            count_value
                     FROM   @ohdsi_database_schema.heracles_results
                     WHERE  analysis_id IN ( 1830 )
                            AND cohort_definition_id = @cohortDefinitionId
                   ) iq1
                   GROUP  BY iq1.cohort_definition_id, iq1.concept_id
                   HAVING Sum(iq1.count_value) > @minCovariatePersonCount) ct1
               ON hr1.cohort_definition_id = ct1.cohort_definition_id 
                  AND hr1.concept_id = ct1.concept_id 

INNER JOIN (
  SELECT iq1.cohort_definition_id, iq1.concept_id, Sum(iq1.count_value)
  FROM   (
    SELECT cohort_definition_id,
      CAST(CASE WHEN isNumeric(stratum_1) = 1 THEN stratum_1 ELSE null END AS INT) AS 
concept_id,
      count_value
    FROM   @ohdsi_database_schema.heracles_results
    WHERE  analysis_id IN ( 1830 )
      AND cohort_definition_id = @cohortDefinitionId
  ) iq1
  GROUP  BY iq1.cohort_definition_id, iq1.concept_id
  HAVING Sum(iq1.count_value) > @minCovariatePersonCount
) ct1 ON hr1.cohort_definition_id = ct1.cohort_definition_id 
  AND hr1.concept_id = ct1.concept_id 

select col1, col2, col3
  col4, col5 -- col4 and col5 are additional expressions to select, so should be indented
from table1 t1 -- indenting is at the same level as select
join table2 t2 on t1.col1 = t2.col1 -- indenting is at  same level as select/from
left join ( -- indenting same level as select/from/join and subquery begins with ( on the  same line
  select col1, col2, 
    MAX(col3) as max_col3 -- indented expression belongs to select
  from table3 t3
  group by col1, col2 -- indented aligned with the select/from of this subquery
) z on z.col1 = t2.col1
order by t1.col1 asc, t1.col1 desc -- indented aligned with the top-level select/from/join that the order by applies to