How to handle hexaploidy of Wheat for vcf file

Question

[hafiz.talhamalik]

I have a GBS data for wheat. I mapped it to reference and then used freebayes for variant calling. it has the option for ploidy. so should I used 6 or 2 ? bcoz as wheat is hexploid but the reference has chromosomes sequences as 1A, 1B and 1C. so keeping in mind I should be using the parameter ploidy with 2. Am I doing it right ? if someone could enlighten me ?

[microfuge]

One way (only my guess) would be to look at genotypes/info available in ensembl plants website for wheat ( https://plants.ensembl.org/Triticum_aestivum/Info/Index a quote from the website "Bread wheat is hexaploid, with a genome size estimated at ~17 Gb, composed of three closely-related and independently maintained genomes " ) . Also looking at genotypes of SNPs in ensembl plants which seem to be standard diploid (https://plants.ensembl.org/Triticum_aestivum/Variation/Population?db=core;g=TraesCS3D02G273600;r=3D:379535906-379539827;t=TraesCS3D02G273600.1;v=BA00408873;vdb=variation;vf=224541 ). Overall my hunch would be that since the subgenomes are present in the reference fasta diploid genotypes would make sense.

[cpad0112]

This is not relevant for your work. But Tassel pipeline is designed for handling wheat GBS data.

[hafiz.talhamalik]

ok..!! May be I m wrong but Tassel is mainly designed for maize which is diploid.

Answer 1

[JC]

Yes, you need to set your ploidy value to 6, this can produce VCFs with more complex representation of variants