Question: paternity and maternity testing
gravatar for ceityk
3.5 years ago by
Iran, Islamic Republic Of
ceityk10 wrote:


I have a reference genome with an annotation data telling locations of genes.

and i have three child, three man and three women reads data.

i want to determine mother and father of each child.

can you help me, please.

i aligned reads using bowtie and then see themes in IGV.

i am familiar with r studio but i don't know what should i do.

do you have any idea about this?


thanks in advance.


alignment bowtie samtools • 969 views
ADD COMMENTlink modified 3.4 years ago by Guy Reeves1.0k • written 3.5 years ago by ceityk10
gravatar for Guy Reeves
3.4 years ago by
Guy Reeves1.0k
Guy Reeves1.0k wrote:


HI khanbaba

​While I have not done what you are trying to do. what  you have done the first part of generating a genotype for each individual.

​The next step  I would suspect would be to phase these genotypes into the  two haplotypes in each gene (for both children and parents).  I think you will not be able to do this in Galaxy (but I may be wrong).  Programs like shapeit or  Beagle  would do the job easily, they can use massive human haplotype reference panels to help do this with a high degree of accuracy (both programs output confidence metrics).  

You would want to do this for each gene separately but including all individuals ( I know shapeit will take .vcf files). Ones you have the  haplotypes of all the individuals involved I guess that it is trivial to identify the parents.

Thanks Guy

PS If you do find a way to phase genotypes within Galaxy please tell me as this is something I might be interested in doing in the future.



ADD COMMENTlink written 3.4 years ago by Guy Reeves1.0k

Nice, Thanks Guy! And I agree, this would be a super interesting workflow to share with others. Either through the Tool Shed and/or Main. If interested and available, either of you could also join us at the Data Hackathon at GCC this year and build it with others! Jen

ADD REPLYlink written 3.4 years ago by Jennifer Hillman Jackson25k

HI Jen 

I will be at the Galaxy Meeting at Norwich, I will try my very best to make the Data Hackathon, so see you there.Thanks Guy

ADD REPLYlink written 3.4 years ago by Guy Reeves1.0k
gravatar for Jennifer Hillman Jackson
3.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:


There is not a Galaxy tutorial that I am aware of that covers this type of analysis. However, reviewing publications that do this would be a good place to start. If an analogous tool/method was used command-line, it could be used in Galaxy. With either existing tools or by wrapping any needed tools. I know of at least one private company that does this exact processing using a custom Galaxy build, but from what I know, all of that is proprietary.

Good luck with your project! If anyone from the community wishes to add in more advice, please do! Jen, Galaxy team

ADD COMMENTlink written 3.5 years ago by Jennifer Hillman Jackson25k
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