finding gene sequence from WGS data

Question

[analyst]

I have performed variant calling and annotation analysis from WGS data. Now I need to get sequences of few genes containing variants.

How can I get sequences of particular variant containing genes?

[cmdcolin]

I know this isn't the exact answer to your question but the most common workflow to see the impact of variants on genes is to run a variant effect predictor

[GenoMax]

OP seems to have at least tried doing this (if it the same data): building snpeff database for plant

[analyst]

Yes I have done variant annotation.

Its rice data, I used available rice database from snpEff.

My PI wants to perform structural analysis too like comparing structure of normal gene structure with annotated gene containing variant.

Therefore I would need to extract gene sequences for only 3 or 4 genes from our WGS data.

Your guidance is highly appreciated.

Thankyou!

Answer 1

[swbarnes2]

It's tricky to get full sequences out of a bam, so your best bet is to make a fixed consensus sequence using your original reference fasta and your vcf.

[analyst]

Thanks swbarnes2!

I need to extract the sequences of 3 or 4 genes only not all genes

[swbarnes2]

It's probably simpler to just make the whole altered consensus, then pick out what you want, instead of only making the consensus for 4 regions. You can also then realign to that consensus and see if your genes of interest look good in IGV.