Distinguish between paternal and maternal chromosomes/reads

Question

[lisadavic66]

Dear All,

What are the computational ways to distinguish between paternal and maternal chromosomes/reads in genomic sequences?

Thanks!

Answer 1

[Pierre Lindenbaum]

• if the read is mapped on chrY, it obviously comes from the father....
• sequence both parents and call the variations. There will be reads carrying specific paternal/maternal genotypes.

[lisadavic66]

Thank you for your help.

If I have a DNA sequence data from a parent and a sequence data from a child, how can I distinguish the chromosomes? Are there some existing methods/software I can use?

Thank you again.

[karl.stamm]

There really is no 'distinguishing chromosomes' in a NGS experiment. They're all chopped, stirred, and amplified before sequencing. All you can do is see what is shared with either parent. You can see if a variant is present in the parent, or not. With only one parent, most of the other mutations will be from the second parent, and some will be new in the offspring.

[lisadavic66]

Thank you for your comments!