paternity and maternity testing

Question: paternity and maternity testing

3.5 years ago by

ceityk • 10

Iran, Islamic Republic Of

ceityk • 10 wrote:

hi,

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.

khanbaba

alignment bowtie samtools • 969 views

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modified 3.4 years ago by Guy Reeves • 1.0k • written 3.5 years ago by ceityk • 10

3.4 years ago by

Guy Reeves • 1.0k

Germany

Guy Reeves • 1.0k 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 COMMENT • link written 3.4 years ago by Guy Reeves • 1.0k

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 REPLY • link written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 3.4 years ago by Guy Reeves • 1.0k

3.5 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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 COMMENT • link written 3.5 years ago by Jennifer Hillman Jackson ♦ 25k

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