text: user2862: In this paper, the authors talk about copy number neutral reads (as reads that equally represent parental chromosomes) and active reads (as reads from only one parent chromosome):
  
  We reasoned that the reads mapped into a genomic window can be partitioned in two sets: one set includes reads that equally represent parental chromosomes (copy number neutral reads); and the other set contains reads from only one parent chromosome (active reads).
  
  Nonetheless, I have some difficulties understanding these two concepts. Can somebody try to expand on what they wrote?
  
  user939: In genetics normally one gets a copy (allele) of a gene (or actually a chromosome) from each parent. If the alleles differ between parents, for example by a SNP, one would have one copy of each allele. With (NGS) sequencing you would get an even amount of reads for both copies. However with somatic mutations, hence mutations which occur after meiosis and gamete forming, one can lose or gain parts of the chromosome (copy number variation). In this situation, some genomic regions might be deleted or amplified. So the allele of one parent can be deleted, leaving you with only the allele of the other parent.
  As requested, I have made a simple drawing of a situation where a region differs between parent alleles with SNPs. After a deletion of one of the allele only reads of the other allele are left.
   
  
original_text: 2862: <p><a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0439-6" rel="nofollow noreferrer">In this paper</a>, the authors talk about <em>copy number neutral reads</em> (as reads that equally represent parental chromosomes) and <em>active reads</em> (as reads from only one parent chromosome):</p>
  
  <blockquote>
    <p>We reasoned that the reads mapped into a genomic window can be partitioned in two sets: one set includes reads that equally represent parental chromosomes (copy number neutral reads); and the other set contains reads from only one parent chromosome (active reads).</p>
  </blockquote>
  
  <p>Nonetheless, I have some difficulties understanding these two concepts. Can somebody try to expand on what they wrote?</p>
   939: <p>In genetics normally one gets a copy (allele) of a gene (or actually a chromosome) from each parent. If the alleles differ between parents, for example by a SNP, one would have one copy of each allele. With (NGS) sequencing you would get an even amount of reads for both copies. However with somatic mutations, hence mutations which occur after meiosis and gamete forming, one can lose or gain parts of the chromosome (copy number variation). In this situation, some genomic regions might be deleted or amplified. So the allele of one parent can be deleted, leaving you with only the allele of the other parent.</p>
  
  <p>As requested, I have made a simple drawing of a situation where a region differs between parent alleles with SNPs. After a deletion of one of the allele only reads of the other allele are left.
  <a href="https://i.stack.imgur.com/AMmw3.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/AMmw3.jpg" alt="enter image description here"></a>   </p>
  