remove option to only output somatic variants

hall-lab · Mar 27, 2015 · d9fca38 · d9fca38
1 parent 7db373d
commit d9fca38
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Showing 2 changed files with 1 addition and 6 deletions.
diff --git 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
@@ -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
                 ;;