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
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.