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finding gene sequence from WGS data

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?

gene wgs
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updated by swbarnes2 swbarnes2 • written by Bushra Bibi Bushra Bibi

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

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written by cmdcolin cmdcolin

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!

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written by Bushra Bibi Bushra Bibi

1 answer

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.

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written by swbarnes2 swbarnes2

Thanks swbarnes2!

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

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written by Bushra Bibi Bushra Bibi

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.

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written by swbarnes2 swbarnes2

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