homopolymer and dinucluotide filter

[huangyuanf]

Hi,
I noticed in the Q&A, you have recommended that For WGS variants, the exclusion of annotated homopolymer and dinucleotide repeats will remove false positives and increase the validation rate, but decrease the sensitivity. But I do not kown what does homopolymer=0 and dinucleotide=0 mean, is it more reliable as it gets closer to zero or less reliable.
What do you recommend?

Thanks

[shishenyxx]

Hi huangyuanf,

Thank you for your question! Homopolymer and dinucleotide repeat annotations are to define whether a variant is close to homopolymer and dinucleotide repeats in the genome, selecting a "0" annotation avoids the issue. However, might also exclude some true positives, as these homopolymers and dinucleotide repeats are where polymerases also tend to make mistakes.

So =0 is more reliable, you can try to remove anything that is not equal to 0.

Best,

Xiaoxu