We know that human genome has 23 pairs of "homologous chromosomes" i.e 46 in total. Homologous chromosomes are not identical. Why there are only 23 chromosomes in hg19.fa?
The hg19.fa contains one reference sequence for every chromosome. Both homologuous chromosomes can be compared to the same reference chromosome. There it would be no use for having two different references for each of the two copies of a chromosome - how would you define which reference to use for each of them?
Note that from the output of the current sequencing techniques you can not know whether a mutation occurred in one chromosome or on its homologuous - you need to apply a technique called phasing to determine it.
because sequencing centers use contigs https://en.wikipedia.org/wiki/Contig to create an assembly: there is only one copy of a DNA and there is no way to know the side the contig.
Furthermore, both homologous sequences would be highly similar.
Because, I think, reference genomes are minimal sets of DNA sequences absolutely required to describe an organism. These differences can be definitely analyzed and provided as a VCF alongside the ref genome, no? Also, if the differences between homologous chromosomes are subject-specific, you'd need to account for that in some manner.
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Hello maniraja2000!
It appears that your post has been cross-posted to another site: http://stackoverflow.com/questions/34486859
This is typically not recommended as it runs the risk of annoying people in both communities.
The one on the stackoverflow is not my post