Question: Should I replace heterozygous variants to make a consensus
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gravatar for deepti1rao
4 months ago by
deepti1rao20
deepti1rao20 wrote:

I want to make a consensus genome by replacing variants. I want to replace homozygous variants in the reference. Is it right to replace the heterozygous variants? The ALT allele must correspond to the homozygous chromosome of a diploid organism. That's my understanding. So I am thinking of not replacing such variants.

ADD COMMENTlink modified 4 months ago • written 4 months ago by deepti1rao20

What is your goal in generating a consensus genome ?

ADD REPLYlink modified 4 months ago • written 4 months ago by Nicolas Rosewick7.3k

Hi! The goal is to do a reference based assembly. 97% of our reads align to the reference.

ADD REPLYlink written 4 months ago by deepti1rao20

So why didn't you use a reference-guided genome assembly (e.g. Velvet, MIRA, Spades, etc..) ?

ADD REPLYlink written 4 months ago by Nicolas Rosewick7.3k

Currently, I do not have enough data to take up a proper assembly. I have tried velvet de novo. When I mapped the resulting contigs to the reference, I found a lot of misassemblies and the coverage is far less than what my reads cover.

I think all the reference based assemblers initially do a de novo assembly and then map the contigs to the reference. So it must be the same method that I've used. I have only paired end data. No mate pairs. Even the paired end data is pooled from different plants, making it 120 x. I am not sure if this kind of a raw data is good enough for a de novo assembly. Since the reference is so close, I rather want to map reads to it directly and replace the variants in it.

ADD REPLYlink written 4 months ago by deepti1rao20

if you want to save information about heterozygosity, you can use IUPAC codes to represent diploid state.

ADD REPLYlink written 4 months ago by Alice270

Thanks for this idea! Are two base codes understood and accepted by tools like Bowtie2, samtools etc for future analyses??

ADD REPLYlink written 4 months ago by deepti1rao20
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