Update README.md

README.md

@@ -91,27 +91,6 @@ mutation in a single patient.  Columns can be in any order, with names and
 formats as follows.  To provide maximal input flexibility, MutSig accepts
 synonyms for each column name.  Column names are case sensitive.
 
-<!--* `chr`: Chromosome of the mutation.  MutSig only analyzes mutations on autosomal or sex chromosomes, and does not consider the mitochondrial chromosome or unplaced/alternate contigs.
-  * Range: `(chr)?[1..24XY]`
-  * Synonyms: `Chromosome`
-
-* `pos`: hg19 position of the mutation, 1-indexed.
-  * Regex: `[0-9]+`
-  * Synonyms: `Position`, `start`, `Start_position`
-
-* `patient`: Unique identifier for the patient.
-  * Regex: `[A-Za-z0-9]+`
-  * Synonyms: `Tumor_Sample_Barcode`, `Patient_name`
-
-* `ref_allele`: hg19 reference base(s) for the position.  In the case of insertions, must be "-".
-  * Regex: `(-|[ACGT]+)`
-  * Synonyms: `Reference_Allele`
-
-* `newbase`: Observed variant allele at the position.  In the case of deletions, must be "-".
-  * Regex: `(-|[ACGT]+)`
-  * Synonyms: `Tumor_Allele`, `Tum_allele`, `Alt_allele`, `Alternate_allele`, `Tumor_Seq_Allele2` -->
-
-Note that MutSig does not require any other mutation annotations; it infers everything else on its own.
 * `chr`: Chromosome of the mutation.  MutSig only analyzes mutations on
          autosomal or sex chromosomes, and does not consider the
          mitochondrial chromosome or unplaced/alternate contigs.
@@ -122,7 +101,7 @@ Note that MutSig does not require any other mutation annotations; it infers ever
   * Regex: `[0-9]+`
   * Synonyms: `Position`, `start`, `Start_position`
 
-* gene: HUGO symbol for the gene containing this mutation, or "Unknown"
+* `gene`: HUGO symbol for the gene containing this mutation, or "Unknown"
         for IGR mutations.
   * Regex: `[A-Za-z0-9]+`
   * Synonyms: `Hugo_Symbol`, `Gene_name`