diff --git a/pyproject.toml b/pyproject.toml
index 3cc8fbd..1561e95 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,6 +13,7 @@ dependencies = [
     "rich>=13.7.1",
     "polars>=1.5.0",
     "ldsc",
+    "igwas",
 ]
 readme = "README.md"
 requires-python = ">= 3.11"
@@ -49,4 +50,5 @@ allow-direct-references = true
 packages = ["src/maxgcp"]
 
 [tool.uv.sources]
-ldsc = { path = "../../Documents/git/ldsc" }
+ldsc = { git = "https://github.com/zietzm/ldsc", branch = "py3" }
+igwas = { git = "https://github.com/tatonetti-lab/indirect-gwas" }
diff --git a/src/maxgcp/cli.py b/src/maxgcp/cli.py
index 1967886..42545d3 100644
--- a/src/maxgcp/cli.py
+++ b/src/maxgcp/cli.py
@@ -9,6 +9,7 @@
 import pandas as pd
 import polars as pl
 import typer
+from igwas.igwas import igwas_files
 from rich.logging import RichHandler
 from rich.progress import track
 
@@ -398,3 +399,78 @@ def fit_command(
     )
     logger.info(f"Writing weights to {output_file}")
     maxgcp_weights_df.to_csv(output_file, sep="\t")
+
+
+@app.command(name="indirect-gwas")
+def run_indirect_gwas(
+    gwas_paths: Annotated[
+        list[Path],
+        typer.Argument(
+            exists=True, help="Path to GWAS summary statistics", show_default=False
+        ),
+    ],
+    projection_coefficient_file: Annotated[
+        Path,
+        typer.Argument(
+            exists=True, help="Path to projection coefficient file", show_default=False
+        ),
+    ],
+    phenotype_covariance_file: Annotated[
+        Path,
+        typer.Argument(
+            exists=True, help="Path to phenotypic covariance file", show_default=False
+        ),
+    ],
+    n_covar: Annotated[
+        int,
+        typer.Option("--n-covar", help="Number of covariates to use"),
+    ],
+    output_file: Annotated[
+        Path,
+        typer.Argument(exists=False, help="Path to output file", show_default=False),
+    ],
+    snp_col: Annotated[str, typer.Option("--snp", help="Name of SNP column")] = "ID",
+    beta_col: Annotated[
+        str, typer.Option("--beta", help="Name of beta column")
+    ] = "BETA",
+    std_error_col: Annotated[
+        str, typer.Option("--std-error", help="Name of standard error column")
+    ] = "SE",
+    sample_size_col: Annotated[
+        str, typer.Option("--sample-size", help="Name of sample size column")
+    ] = "OBS_CT",
+    compress: Annotated[
+        bool, typer.Option("--compress", help="Compress output file")
+    ] = True,
+    use_stem: Annotated[
+        bool, typer.Option(help="Use stem of GWAS file as phenotype name")
+    ] = True,
+    chunksize: Annotated[
+        int, typer.Option("--chunksize", help="Chunksize for IGWAS")
+    ] = 100_000,
+    n_threads: Annotated[
+        int, typer.Option("--n-threads", help="Number of threads for IGWAS")
+    ] = 1,
+):
+    """Compute GWAS summary statistics for a projected phenotype."""
+    if not use_stem:
+        raise NotImplementedError(
+            "Indirect GWAS only currently supports GWAS files where the file "
+            "stem represents the phenotype"
+        )
+    igwas_files(
+        projection_matrix_path=projection_coefficient_file.as_posix(),
+        covariance_matrix_path=phenotype_covariance_file.as_posix(),
+        gwas_result_paths=[p.as_posix() for p in gwas_paths],
+        output_file_path=output_file.as_posix(),
+        num_covar=n_covar,
+        chunksize=chunksize,
+        variant_id=snp_col,
+        beta=beta_col,
+        std_error=std_error_col,
+        sample_size=sample_size_col,
+        num_threads=n_threads,
+        capacity=n_threads,
+        compress=compress,
+        quiet=True,
+    )
diff --git a/uv.lock b/uv.lock
index c15a24b..111eba3 100644
--- a/uv.lock
+++ b/uv.lock
@@ -109,10 +109,20 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/d1/d6/3965ed04c63042e047cb6a3e6ed1a63a35087b6a609aa3a15ed8ac56c221/colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6", size = 25335 },
 ]
 
+[[package]]
+name = "igwas"
+version = "0.1.0"
+source = { git = "https://github.com/tatonetti-lab/indirect-gwas#3b85a937d0b13494378eecab4f25f3ffc1f787fd" }
+dependencies = [
+    { name = "numpy" },
+    { name = "pandas" },
+    { name = "zstandard" },
+]
+
 [[package]]
 name = "ldsc"
 version = "0.1.0"
-source = { directory = "../../Documents/git/ldsc" }
+source = { git = "https://github.com/zietzm/ldsc?branch=py3#a6305d51deea71680de764288c977e5e648aca10" }
 dependencies = [
     { name = "bitarray" },
     { name = "numpy" },
@@ -123,20 +133,6 @@ dependencies = [
     { name = "zstandard" },
 ]
 
-[package.metadata]
-requires-dist = [
-    { name = "bitarray", specifier = ">=2.9.2" },
-    { name = "numpy", specifier = ">=2.1.0" },
-    { name = "pandas", specifier = ">=2.2.2" },
-    { name = "pybedtools", specifier = ">=0.10.0" },
-    { name = "pyzstd", specifier = ">=0.16.1" },
-    { name = "scipy", specifier = ">=1.14.1" },
-    { name = "zstandard", specifier = ">=0.23.0" },
-]
-
-[package.metadata.requires-dev]
-dev = [{ name = "pytest", specifier = ">=8.3.2" }]
-
 [[package]]
 name = "markdown-it-py"
 version = "3.0.0"
@@ -154,6 +150,7 @@ name = "maxgcp"
 version = "0.1.2"
 source = { editable = "." }
 dependencies = [
+    { name = "igwas" },
     { name = "ldsc" },
     { name = "numpy" },
     { name = "pandas" },
@@ -165,7 +162,8 @@ dependencies = [
 
 [package.metadata]
 requires-dist = [
-    { name = "ldsc", directory = "../../Documents/git/ldsc" },
+    { name = "igwas", git = "https://github.com/tatonetti-lab/indirect-gwas" },
+    { name = "ldsc", git = "https://github.com/zietzm/ldsc?branch=py3" },
     { name = "numpy", specifier = ">=1.26.4" },
     { name = "pandas", specifier = ">=2.2.2" },
     { name = "polars", specifier = ">=1.5.0" },