Question: Mutation position on sequencing read length
gravatar for rahulk.aiims
2.6 years ago by
rahulk.aiims0 wrote:

Dear All,

I have a question regarding next generation sequencing data. I have somatic mutations called using MuTect. I just want to know the position of these mutations according to the read length i.e. if I have reads of length 150 bases, where a given mutation is present from position 1 - 150.

Is there any way to calculate this?

Many thanks, Rahul

ADD COMMENTlink written 2.6 years ago by rahulk.aiims0

Hello Rahul,

could please explain why you need this information?

If the DNA was randomly fragmented during the library prep, the position will be different in nearly every read that span the position of your mutation. In case the library prep is amplicon based, the position will be the same in every read (as long as there is no second amplicon that span the same region).

A solution would be, to first extract all reads that overlap the position and calculate than the position of the mutation within the read based on the alignment informations.

But before starting this, let's find out whether this is really what you need.

fin swimmer

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by finswimmer14k

Hi Fin,

Thanks for your reply, actually for my FFPE samples I am getting around ~200,000 somatic mutations, which is very weird. I am expecting that because read quality is not good so may be that's why I am getting many mutations from read end position. That's why I want to calculate the average position of each mutation from 5' or 3' end of the supporting reads.

Let me know if you have any thoughts on this.

Many thanks, Rahul

ADD REPLYlink written 2.6 years ago by rahulk.aiims0

Hello Rahul,

so question is about whether your variants are true or false positive. What was your variant caller? The vcf entry could give information to decide whether you have false positive. You should post the header and the first 10 variants within your vcf. Than we can look into more details.

fin swimmer

ADD REPLYlink written 2.6 years ago by finswimmer14k
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