Local Realignment And Local De Novo Assembly Software

Question

[lyz10302012]

Hi everyone,

Are there any softwares to do local realignment or local de novo assembly for the regions that users can specify arbitrarily, not just the regions near indels in dbsnp?

Thanks

[Erik Garrison]

The realignment process ogap will work everywhere. The default left alignment methods in callers like freebayes will also handle much of the issues that arise through misalignment around indels. I would be cautious with the targeted realignment you're talking about, as many of the indles in dbSNP are of very low quality, and the methods to detect these from NGS data are only now maturing.