diff --git a/README.md b/README.md
index c0fd313..d9bb185 100644
--- a/README.md
+++ b/README.md
@@ -289,7 +289,6 @@ tumor.bam         tumor BAM file(s) (comma separated BAMs for multiple libraries
                    we recommend using the annotations/ceph18.b37.include.2014-01-15.bed
                    (see Annotations)
 -t INT           number of threads to use [default: 1]
--s               only output somatic variants
 -F FLOAT         require at least this fraction of observations supporting
                    an alternate allele within a single individual in order
                    to evaluate the position [0.05]
diff --git a/bin/speedseq b/bin/speedseq
index cd60426..0d3dfe0 100755
--- a/bin/speedseq
+++ b/bin/speedseq
@@ -794,7 +794,6 @@ options:
          -o STR   output prefix [tumor.bam]
          -w FILE  BED file of windowed genomic intervals
          -t INT   threads [1]
-         -s       only output somatic variants
          -F FLOAT Require at least this fraction of observations supporting
                     an alternate allele within a single individual in order
                     to evaluate the position [0.05]
@@ -836,7 +835,7 @@ options:
     VERBOSE=0
     KEEP=0
 
-    while getopts ":ho:w:t:F:C:T:Aq:S:svkK:" OPTION
+    while getopts ":ho:w:t:F:C:T:Aq:S:vkK:" OPTION
     do
         case "${OPTION}" in
             h)
@@ -870,9 +869,6 @@ options:
 	    S)
 		SSC_THRES="$OPTARG"
 		;;
-	    s)
-		ONLY_SOMATIC=1
-		;;
             v)
                 VERBOSE=1
                 ;;