Improved README

README.md

@@ -25,12 +25,12 @@ The fields are explained below:
 | Genotype          | Genotype call                                                  |   
 | Filter            | Filters on the genotype call                                   |   
 
-A genotype of "None" indicates a no-call.
-There are currently four possible values for the Filter column:
--PASS: a passing, confident call.  
--More_than_one_possible_genotype: In rare cases, Cyrius reports two possible genotypes for which it cannot distinguish one from the other. These are different sets of star alleles that result in the same set of variants that cannot be phased with short reads, e.g. `*1/*46` and `*43/*45`. The two possible genotypes are reported together, separated by a semicolon.   
--Not_assigned_to_haplotypes: In a very small portion of samples with more than two copies of CYP2D6, Cyrius calls a set of star alleles but they can be assigned to haplotypes in more than one way. Cyrius reports the star alleles joined by underscores. For example, `*1_*2_*68` can be `*1+*68/*2`, `*2+*68/*1` or `*1+*2/*68`. As another example, Cyrius reports `*1x4`, for which the diplotype can be `*1/*1x3` or `*1x2/*1x2`.  
--LowQ_high_CN: In rare cases, at high copy number (>=6 copies of CYP2D6), Cyrius uses less strict approximation in calling copy numbers to account for higher noise in depth and thus the genotype call could be lower confidence than usual.     
+A genotype of "None" indicates a no-call.  
+There are currently four possible values for the Filter column:  
+-`PASS`: a passing, confident call.   
+-`More_than_one_possible_genotype`: In rare cases, Cyrius reports two possible genotypes for which it cannot distinguish one from the other. These are different sets of star alleles that result in the same set of variants that cannot be phased with short reads, e.g. `*1/*46` and `*43/*45`. The two possible genotypes are reported together, separated by a semicolon.   
+-`Not_assigned_to_haplotypes`: In a very small portion of samples with more than two copies of CYP2D6, Cyrius calls a set of star alleles but they can be assigned to haplotypes in more than one way. Cyrius reports the star alleles joined by underscores. For example, `*1_*2_*68` can be `*1+*68/*2`, `*2+*68/*1` or `*1+*2/*68`. As another example, Cyrius reports `*1x4`, for which the diplotype can be `*1/*1x3` or `*1x2/*1x2`.  
+-`LowQ_high_CN`: In rare cases, at high copy number (>=6 copies of CYP2D6), Cyrius uses less strict approximation in calling copy numbers to account for higher noise in depth and thus the genotype call could be lower confidence than usual.     
 
 A .json file is also produced that contains more information about each sample.