Question: SNP analysis of Allotetraploid genome
gravatar for GirKir1424
3 months ago by
GirKir142480 wrote:

Hi All Recently i got whole genome seq data of allotetraploid genome(Plant) generated from illumina the basic pipleine which i am following is
1)Fastqc (Quality check) 2)Trimming if required 3)Mapping against reference 4)Snp Call using GATK or Samtools 5)Snp prirotization using SnpEff

My query is what all check points i need to make to get better results. and how I will be interpreting snps from allotetrapoid genome from vcf file. If any experienced answer will be highly appreciated

Thank You!!!

ADD COMMENTlink modified 6 weeks ago by Biostar ♦♦ 20 • written 3 months ago by GirKir142480

If it is an allotetraploid (is it durum wheat? :P) then you treat each homoeologous genome as a diploid. Think carefully about trimming, though. You want to remove adapter contamination and then filter low quality reads. Especially if you have a highly repetitive genome, you don't want to lose too much length in order to not generate misaligned reads. The most quality trimming should be to get rid off < phred 3 bases on the ends. For calling you can also use freebayes. And for SNP effect prediction (and thus prioritization) you can also have a look into VEP - Variant Effect Predictor.

ADD REPLYlink written 6 weeks ago by cschu181670

Hi @cschu181 How should i treat homoelogous as diploid i have reference genome of samples (Cotton AADD type ).

ADD REPLYlink modified 19 days ago • written 19 days ago by GirKir142480

In the case of allotetraploids, you're not dealing with 4 copies of the same chromosome. Instead, you treat A and D chromosomes as different entities, with 2 copies each. In practice, this means that if your SNP Caller allows you to set ploidy, then you can set it to (or leave it at) diploid. For, say, potato, you'd set ploidy to 4, as it is a (non-allo)-tetraploid.

ADD REPLYlink written 17 days ago by cschu181670

So you meant to say in my freebayes tool I have to set ploidy parameter as 2 rather 4 right !!

ADD REPLYlink written 17 days ago by GirKir142480

Yes, and in GATK Haplotype Caller you can leave the default setting of 2.

ADD REPLYlink written 16 days ago by cschu181670
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 613 users visited in the last hour