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# I want to know if GATK can do what I want! NGS reads, polyploids, phylogeny

Member
edited January 2013

Hello,
I have 454 reads of loci on polyploid individuals. I am able to produce assemblies containing the different copies of one locus per individual. But I want to extract the reads corresponding to each copies, to then be able to produce phylogenies.
Does the GATK can do something like this?

Thanks,

• Charlestown, MAMember

You can use the GATK as a framework to develop tools like that, but we do not provide any tools for genome assembly or phylogenies.

Is your data in a BAM file?

• Member

I don't intend to do the phylogeny through GATK, and I don't have genome data, just a few loci ranging in size between 700 and 2500 bp. I need something using the Linkage Disequilibrium between SNP to produce assemblies containing only one kind of copy.

Is BAM suitable for assembled reads?

• Charlestown, MAMember

If you need to call SNPs, you can use the GATK (take a look at the best practices document for calling variants).

With the variants called you can use your favorite program for linkage disequilibrium and phylogeny generation.

• Member

I came to this software because I thought that what you call "haplotype/genotype caller" is what I want to do. Did I mistaken? Could you tell me what these modules do and how the output look like?