What Genetic Marker To Use To Infer Pedigree From Sequencing Data?

Question

[michealsmith]

Here's a unusual tricky question.

Now I've got whole-exome sequencing data for 5 individuals from a family. However we don't know the pedigree. I'm just curious any way to infer the pedigree based on sequencing data? What genetic marker to look at? (For example, what I can think of is the number-variable tandem repeats...)

Thanks

Answer 1

[Zev.Kronenberg]

You can use:

http://jorde-lab.genetics.utah.edu/ersa/

[michealsmith]

thanks, but seems ERSA package is not downloadable..

[Zev.Kronenberg]

http://jorde-lab.genetics.utah.edu/ersa/ERSA_distr_1.0/

Answer 2

[Larry_Parnell]

If you have sequencing data, you have haplotypes, Haplotypes are quite useful for this task.

[michealsmith]

thx. what how can I find the haplotypes from sequencing data?

Answer 3

[matted]

You might consider the methods described in this paper: Detection of identity by descent using next-generation whole genome sequencing data

If you are committed to tandem repeats, you could use the methods in this paper: lobSTR: A short tandem repeat profiler for personal genomes

Answer 4

[piper.below]

Try PRIMUS https://primus.gs.washington.edu/primusweb/