Is there any tool can identify which copy of chromosome reads coming from?

Question

[qyang]

Every chromosome has two copies. When reads are mapping back to the genome, the reads come from the same region of different copies could have some difference. So does the aligner or other tools can know which copy some reads coming from?

Answer 1

[Brian Bushnell]

The reference is a haploid representation of the genome. It is generally impossible to determine which copy a read mapped to using the haploid reference. But in situations where there is heterozygosity, it may be possible to determine which copy a read mapped to. You may want to construct an alternative reference and map to both simultaneously, and assign reads accordingly. This is not perfect, though, since most reads will probably map ambiguously to both references.