You can easily reconcile by using Excel download GSTR 2A of all the month in Excel format and consolidate all into one sheet. make pivot table w.r.t. each GSTN then use vlookup to find out the total purchase in your books w.r.t. each GSTN for particular year if total of particular GSTN matched - reconciliation if not - then check invoice wise for this you to use concatenate formula on GSTN column and Invoice column in both(GSTR2A & Books purchase ) excel file now use vlookup to find out invoice wise purchase in GSTR2A sheet. if matched - reconcile not - report
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