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No reference genome (de novo SNP calling)

sstwins21sstwins21 New ZealandMember

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

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