strand-biased mutation analysis on WES data

Question

[shiyang93]

I have some WES data of liver cancer, and I have got the somatic mutations.

Now I want to know how to determine these mutations are on which strand(transcribed/untranscribed strand). For example, if I have a mutation on forward strand: chr1 123456, how can I know its strand information?

Could anyone give me some advice, or is there a software to do the work?

Thanks!

[WouterDeCoster]

That would require your WES protocol to be stranded, which I haven't heard from yet. So that's the first thing to check. If you have a standard exome sequencing prep, strandedness is not preserved.

Secondly, does it make sense to look for strandedness in transcribed/untranscribed strand? Don't you expect a mutation to be present in both strands of the chromosome? Unless you're looking at an unfixed mismatch, but if I'm not mistaken these get repaired quite quickly.

[Gene_MMP8]

So if I want to extract fasta sequence of the flanking regions around mutations (SNVs), I should just consider all the mutations to be in one particular strand and go ahead with the analysis (bedtools getfasta), right?