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

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

genetics
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updated by Ram Ram • written by michealsmith michealsmith

4 answers

You can use:

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

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written by Zev.Kronenberg Zev.Kronenberg

thanks, but seems ERSA package is not downloadable..

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written by michealsmith michealsmith

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

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written by Larry_Parnell Larry_Parnell

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

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written by michealsmith michealsmith

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

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updated by Ram Ram • written by matted matted

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

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updated by Ram Ram • written by piper.below • piper.below

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