Use Freebayes parameters in use for 1000 genomes calling

bcbio · May 16, 2012 · 680ebb3 · 680ebb3
1 parent 0ab42fd
commit 680ebb3
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/bcbio/variation/freebayes.py b/bcbio/variation/freebayes.py
@@ -37,7 +37,7 @@ def run_freebayes(align_bam, ref_file, config, dbsnp=None, region=None,
         with file_transaction(out_file) as tx_out_file:
             cl = [config["program"].get("freebayes", "freebayes"),
                   "-b", align_bam, "-v", tx_out_file, "-f", ref_file,
-                  "--left-align-indels"]
+                  "--left-align-indels", " --no-filters", "--use-mapping-quality"]
             cl += _freebayes_options_from_config(config["algorithm"], out_file, region)
             subprocess.check_call(cl)
     return out_file