diff probvalueforhetero.xml @ 2:d5ed5c2e25c3 draft

Uploaded

--- a/probvalueforhetero.xml	Wed Apr 01 17:06:29 2015 -0400
+++ b/probvalueforhetero.xml	Wed Apr 22 12:48:40 2015 -0400
@@ -28,8 +28,8 @@
 
 **What it does**
 
-- This tool will calculate the probability that the allele combination can generated the given read profile. This tool is part of the pipeline to estimate minimum read depth.
-- The calculation of probability is very similar to the tool **Correct genotype for microsatellite errors**. However, this tool will restrict the calculation to only the allele combination indicated in input. Also, when it encounter allele combination that cannot be generated from error profile, the total probability will be zero instead of using base substitution rate. 
+- This tool will calculate the probability that the allele combination can generated the given the STR length profile. This tool is part of the pipeline to estimate minimum read depth.
+- The calculation of probability is very similar to the tool **Correct genotype for STR errors**. However, this tool will restrict the calculation to only the allele combination indicated in input. Also, when it encounter allele combination that cannot be generated from error profile, the total probability will be zero instead of using base substitution rate. 
 
 **Citation**
 
@@ -37,25 +37,25 @@
  
 **Input**
 
-The input format is the same as output from **Correct genotype for microsatellite errors** tool.
+The input format is the same as output from **Correct genotype for STR errors** tool.
 
-- Column 1 = location of microsatellite locus. 
-- Column 2 = length profile (length of microsatellite in each read that mapped to this location in comma separated format). 
-- Column 3 = motif of microsatellite in this locus. The input file can contain more than three column. 
-- Column 4 = homozygous/heterozygous label.
-- Column 5 = log based 10 of (the probability of homozygous/the probability of heterozygous)
-- Column 6 = Allele for most probable homozygous form.
-- Column 7 = Allele 1 for most probable heterozygous form.
-- Column 8 = Allele 2 for most probable heterozygous form.
+- Column 1 = location of STR locus. 
+- Column 2 = length profile (length of STR in each read that mapped to this location in comma separated format). 
+- Column 3 = motif of STR in this locus. The input file can contain more than three column. 
+- Column 4 = homozygote/heterozygote label.
+- Column 5 = log based 10 of (the probability of homozygote/the probability of heterozygote)
+- Column 6 = Allele for most probable homozygote.
+- Column 7 = Allele 1 for most probable heterozygote.
+- Column 8 = Allele 2 for most probable heterozygote.
 
 Only column 2,3,7,8 were used in calculation. 
 
 **Output**
 
 
-The output will be contain original eight column from the input. However, it will also add these following columns. 
+The output will contain the original eight columns from the input and the following additional columns. 
 - Column 9 = Probability of the allele combination to generate given read profile.
-- Column 10 = Number of possible rearrangement of given read profile.
+- Column 10 = Number of possible rearrangements of the given read profile.
 - Column 11 = Probability of the allele combination to generate read profile with any rearrangement (Product of column 9 and column 10)
 - Column 12 = Read depth