diff --git a/HISTORY.md b/HISTORY.md
index 7e86bc925..6c206ccf0 100644
--- a/HISTORY.md
+++ b/HISTORY.md
@@ -1,5 +1,8 @@
 ## 1.1.1 (in progress)
 
+- tumor-only prioritization: do not apply LowPriority filter by default, instead
+  annotate with external databases. Use `tumoronly_germline_filter` to re-enable
+  previous behavior.
 - gemini: databases no longer created by default. Use `tools_on: [gemini]` or
   `tools_on: [gemini_orig]` to create a database.
 - vcfanno: run gemini and somatic annotations by default, producing annotated
diff --git a/bcbio/variation/prioritize.py b/bcbio/variation/prioritize.py
index 5e6fcc07e..fa46074d2 100644
--- a/bcbio/variation/prioritize.py
+++ b/bcbio/variation/prioritize.py
@@ -15,11 +15,11 @@
 import csv
 import re
 
-from bcbio import install, utils
+from bcbio import utils
 from bcbio.distributed.transaction import file_transaction
 from bcbio.pipeline import datadict as dd
 from bcbio.provenance import do
-from bcbio.variation import population, vcfanno, vcfutils
+from bcbio.variation import population, vcfutils
 
 geneimpacts = utils.LazyImport("geneimpacts")
 cyvcf2 = utils.LazyImport("cyvcf2")
@@ -33,7 +33,7 @@ def handle_vcf_calls(vcf_file, data, orig_items):
         ann_vcf = population.run_vcfanno(vcf_file, data)
         if ann_vcf:
             priority_file = _prep_priority_filter_vcfanno(ann_vcf, data)
-            return _apply_priority_filter(vcf_file, priority_file, data)
+            return _apply_priority_filter(ann_vcf, priority_file, data)
         # No data available for filtering, return original file
         else:
             return vcf_file
@@ -45,14 +45,19 @@ def _apply_priority_filter(in_file, priority_file, data):
     if not utils.file_exists(out_file):
         with file_transaction(data, out_file) as tx_out_file:
             header = ('##INFO=<ID=EPR,Number=.,Type=String,'
-                      'Description="Prioritization based on external annotations">')
+                      'Description="Somatic prioritization based on external annotations, '
+                      'identify as likely germline">')
             header_file = "%s-repeatheader.txt" % utils.splitext_plus(tx_out_file)[0]
             with open(header_file, "w") as out_handle:
                 out_handle.write(header)
+            if "tumoronly_germline_filter" in dd.get_tools_on(data):
+                filter_cmd = ("bcftools filter -m '+' -s 'LowPriority' "
+                              """-e "EPR[*] != 'pass'" |""")
+            else:
+                filter_cmd = ""
             cmd = ("bcftools annotate -a {priority_file} -h {header_file} "
                    "-c CHROM,FROM,TO,REF,ALT,INFO/EPR {in_file} | "
-                   "bcftools filter -m '+' -s 'LowPriority' "
-                   """-e "EPR[*] != 'pass'" | bgzip -c > {tx_out_file}""")
+                   "{filter_cmd} bgzip -c > {tx_out_file}")
             do.run(cmd.format(**locals()), "Run external annotation based prioritization filtering")
     vcfutils.bgzip_and_index(out_file, data["config"])
     return out_file
@@ -145,12 +150,10 @@ def _calc_priority_filter(row, pops):
 
     - Pass high/medium impact variants not found in population databases
     - Pass variants found in COSMIC or Clinvar provided they don't have two
-      additional reasons to filter (low severity or found in multiple external populations)
+      additional reasons to filter (found in multiple external populations)
     """
     filters = []
     passes = []
-    if row.get("impact_severity") in ["LOW"]:
-        filters.append("lowseverity")
     passes.extend(_find_known(row))
     filters.extend(_known_populations(row, pops))
     if len(filters) == 0 or (len(passes) > 0 and len(filters) < 2):
diff --git a/docs/contents/configuration.rst b/docs/contents/configuration.rst
index 3cd475ba1..1a269ed96 100644
--- a/docs/contents/configuration.rst
+++ b/docs/contents/configuration.rst
@@ -1083,6 +1083,10 @@ lists with multiple options:
   - ``qualimap_full`` runs Qualimap with full bam files but it may be slow.
   - ``damage_filter`` annotates low frequency somatic calls in INFO/DKFZBias for
     DNA damage artifacts using `DKFZBiasFilter <https://github.com/eilslabs/DKFZBiasFilter>`_.
+  - ``tumoronly_germline_filter`` applies a ``LowPriority`` filter to tumor-only calls
+    that match population germline databases. The default is to just apply a tag
+    ``EPR`` (external prioritization) that flags variants present in external
+    databases. Anything missing a ``pass`` here is a likely germline.
   - ``vqsr`` makes GATK try quality score recalibration for variant filtration,
     even for smaller sample sizes.
   - ``svplots`` adds additional coverage and summary plots for CNVkit and detected