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Created 2016-05-27 23:06:21 | Updated | Tags: reference mapping assembly snp-calling

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Hi GATK team,

I am new to bioinformatics and could you help me with this problem?

I am trying to call SNPs on my polyploid samples, consisting of diploids and triplods. But I used a reference genome from a relative species that is a diploid. For this reason, I think all my SNPs only show diploid alleles even for the triploid samples. Thus I want to create my own reference genome by assembling the representative samples (mix of trploids and diploids) like shown in the GATK slide.

I have done mapping before using bwa or bowtie, but I do not know how to assemble using my own samples... This may not be the GATK problem, but could you help me how I can assemble my own reference genome please? Thank you.

Kind regards, Shane

Created 2013-03-13 10:18:39 | Updated 2013-03-13 10:19:56 | Tags: unifiedgenotyper snp reference assembly

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The Unified Genotyper calls SNPs relative to the specified, publicly-available reference assembly.

How can I call SNPs (in many samples, with UG) relative to an in-house individual, which I have sequenced at high-coverage?

My current solution is to perform a de novo assembly on the in-house reference individual using e.g. Velvet, and then simply use the fasta as the reference for UG.

Can the publicly-available reference assembly still be useful here for speeding up the mapping and filling-in missing parts ?

My organism is Drosophila melanogaster.