Homopolymer Errors

[JeanMiCarter]

Hi Jason,

Would you mind clarifying how the program identifies homopolymers indels? For example how many bases are required either side of the indel to be classified? Many thanks!

Jean-Michel

[jason-weirather]

Hi Jean-Michel,

AlignQC identifies homopolymer indels from the alignment string in format such as

AAT-CCCGGTTC - Query AATTC-CGG--C - Reference

By decomposing the alignment into homopolymer blocks

AA T- CCC GG TT C - Query AA TT C-C GG -- C - Reference

Now for homopolymer blocks where a base is called in both query and reference but the counts differ, this is considered a homopolymer error. We can see a single homopolymer deletion in the first T base, and we can see a single homopolymer insertion in the first C base. Note however the second T base in the query has two T insertions, but this would not be called as a homopolymer insertion because it has no equivelent in the reference.

Another way to think of what I am calling a homopolymer indel would be that if both query and reference were homoplymer compressed:

ATCGTC - Query ATCG-C - Reference

any homopolymer indels would no longer show up in the alignment. since they have a 1:1 correspondence between the query and the reference.

I hope that's helpful. Thanks!

Jason

[JeanMiCarter]

Excellent, that's very helpful & informative. Thanks Jason!