--- a/allele-counts.xml	Fri May 31 12:34:28 2013 -0400
+++ b/allele-counts.xml	Tue Jun 04 00:16:29 2013 -0400
@@ -17,21 +17,19 @@
 
   <help>
 
+.. class:: infomark
+
+**What it does**
+
+This tool parses variant counts from a special VCF file (normally the output of the **Naive Variant Detector** tool). It counts simple (ACGT) variants, calculates numbers of alleles, and calculates minor allele frequency. It applies filters based on coverage, strand bias, and minor allele frequency cutoffs.
+
+-----
+
 .. class:: warningmark
 
 **Note**
 
-This will only process a special type of VCF file. The VCF must have a special genotype field in the sample columns, giving the number of each type of variant. Also, the variant data **must be stranded**.
-
-The Naive Variant Detector tool produces this VCF format, and is the normal upstream tool from this one.
-
------
-
-.. class:: infomark
-
-**What it does**
-
-This tool parses variant counts from a special VCF file (normally the output of the Naive Variant Detector tool). It counts simple (ACGT) variants, calculates numbers of alleles, and calculates minor allele frequency. It applies filters based on coverage, strand bias, and minor allele frequency cutoffs.
+The VCF must have a certain genotype field in the sample columns, giving the read count of each type of variant. Also, the variant data **must be stranded**. The **Naive Variant Detector** tool produces this type of VCF.
 
 -----
 
@@ -54,9 +52,16 @@
     11. MINOR   - Minor allele base (2nd most prevalent variant)
     12. MINOR.FREQ.PERC. - Frequency of minor allele
 
-**Example**::
-    SAMPLE   CHR   POS    A   C   G  T  CVRG  ALLELES  MAJOR  MINOR  MINOR.FREQ.PERC.
-    BLOOD_3  chr7  10980  11  88  1  0  100   2        C      A      0.11
+**Example**
+
+This is the header line, followed by some example data lines. Note that some samples and/or sites will not be included in the output, if they fall below the coverage threshold::
+
+    #SAMPLE  CHR    POS  A   C    G    T  CVRG  ALLELES  MAJOR  MINOR  MINOR.FREQ.PERC.
+    BLOOD_1  chr20  99   0   101  1    2  104   1        C      T      0.01923
+    BLOOD_2  chr20  99   82  44   0    1  127   2        A      C      0.34646
+    BLOOD_3  chr20  99   0   110  1    0  111   1        C      G      0.009
+    BLOOD_1  chr20  100  3   5    100  0  108   1        G      C      0.0463
+    BLOOD_3  chr20  100  1   118  11   0  130   0        C      G      0.08462
 
 -----
 
@@ -68,19 +73,15 @@
 
 **N.B.**: This means the total coverage for each printed site will be at least twice the number you give in the "coverage threshold" option.
 
-Also, reads supporting a variant outside the canonical 4 nucleotides will not count towards the coverage requirement. For instance, a site covered by 150 reads on each strand, the majority of which support an indel variant, will not be printed.
+Also, reads supporting a variant outside the canonical 4 nucleotides will not count towards the coverage requirement. For instance, a site/sample line with 100x coverage, all of which support a deletion variant, will not be printed.
 
-Alleles are only counted in the column 9 tally if they meet or exceed the minor allele frequency threshold. In addition, the alleles passing the threshold on each strand have to match (though not in order). Otherwise, the allele count will be 0. The reported minor allele and minor allele frequency, though, will always be reported.
-
-However, if there is a tie for the minor allele (between the 2nd and 3rd most common alleles), the minor allele will be reporated as 'N', and the frequency as 0.
+Alleles are only counted (in column 9) if they meet or exceed the minor allele frequency threshold. So a site/sample line with types of variants, 96% A, 3.3% C, and 0.7% G, will count as 2 alleles (at 1% threshold).
 
------
-
-.. class:: infomark
+Strand bias: the alleles passing the threshold on each strand have to match (though not in order). Otherwise, the allele count will be 0. So a site/sample line whose + strand shows 70% A, 27% C, and 3% G, and - strand shows 70% A and 30% C will have an allele count of 0. The minor allele and minor allele frequency, though, will always be reported\*.
 
-**Additional notes**
+But in this version, there is no requirement that the strands show similar allele frequencies, as long as they both pass the threshold.
 
-
+\*One specific case will actually affect the reported minor allele identity and frequency. If there is a tie for the minor allele (between the 2nd and 3rd most common alleles), the minor allele will be reporated as 'N', and the frequency as 0.0.
 
   </help>