Does A Large Variation In Insert Sizes For Paired End Illumina Sequencing Affect Snp Calling?

Question

[Kevin]

Qn: does a large variation in insert sizes for paired end Illumina sequencing affect SNP calling?

If the purpose is looking for indels I suppose if there's a large variation in insert sizes then you basically have dubious data. I am not so sure about resequencing applications, but I had assumed that when a read can't be mapped properly due to odd insert sizes it will be culled at some stage of a QC filter.

Am I wrong to say that?

Answer 1

[Istvan Albert]

As you mention a larger insert size allows for better positioning of the mate pairs.

That being said unmapped mates or large inserts do not necessarily mean bad data, larger scale rearrangements and copy number variation may also show up as unmapped mate pairs or inserts of unexpected sizes and distributions.

As for wether having a large variation of insert sizes - it is not clear how large are we talking about. The methodology has certain inherent limits on what the insert size can possibly be, but what we see is only where it maps relative to a target reference.