diff --git a/bin/scan2 b/bin/scan2
index de1de43..a0211ba 100755
--- a/bin/scan2
+++ b/bin/scan2
@@ -88,6 +88,7 @@ scan2_param_defaults = {
     'resources': '/opt/anaconda1anaconda2anaconda3/lib/scan2/resources',  # also a directory
     'bam_map': {},             # maps sample name -> bam path
     'amplification_map': {},   # map sample name -> bulk|MDA|PTA|other things in the future..
+    'no_combine_permutations': False,
     'permtool_config_map': {},
     'permtool_matrix_map': {},
     'permtool_n_permutations': 10000,
@@ -1226,6 +1227,8 @@ if __name__ == "__main__":
         help='Similar to --permtool-snv-generation-param but acts as a multiplier for a hard-coded base number of random indels to generate per iteration.')
     permtool.add_argument('--permtool-bedtools-genome-file', type=readable_file, metavar='PATH',
         help='Genome file formatted for the -g option of bedtools intersect.')
+    permtool.add_argument('--no-combine-permutations', default=False, action='store_true',
+        help='Do not combine all per-sample permutations into a single permutation object. When many arbitrary combinations of samples are of interest, it is better to only generate per-sample permutation objects without a final combine step. The per-sample results are stored in the output directory perms_by_sample/SAMPLE_NAME/*.rda, which can be combined in arbitrary groups using scripts/combine_permutations.R.')
 
 
 
diff --git a/snakemake/Snakefile b/snakemake/Snakefile
index 200b41a..b779320 100644
--- a/snakemake/Snakefile
+++ b/snakemake/Snakefile
@@ -39,9 +39,19 @@ if config['analysis'] == 'rescue':
 
 if config['analysis'] == 'permtool':
     include: "snakefile.permtool"
-    rule permtool:
-        input:
-            expand("perms_{muttype}_{passtype}.rda",
-                muttype=[ 'snv', 'indel' ], passtype=[ 'pass', 'rescue' ]),
-            expand("seedinfo_{muttype}_{passtype}.rda",
-                muttype=[ 'snv', 'indel' ], passtype=[ 'pass', 'rescue' ])
+    # Allow user to skip the final combine stage. In this mode, the user just
+    # wants access to all of the individual permutation objects so they can
+    # combine them in arbitrary ways.
+    if config['no_combine_permutations']:
+        rule permtool:
+            input:
+                expand("perms_by_sample/{sample}/{muttype}_{passtype}.rda",
+                    sample=config['permtool_config_map'].keys(),
+                    muttype=[ 'snv', 'indel' ], passtype=[ 'pass', 'rescue' ])
+    else:
+        rule permtool:
+            input:
+                expand("perms_{muttype}_{passtype}.rda",
+                    muttype=[ 'snv', 'indel' ], passtype=[ 'pass', 'rescue' ]),
+                expand("seedinfo_{muttype}_{passtype}.rda",
+                    muttype=[ 'snv', 'indel' ], passtype=[ 'pass', 'rescue' ])