Agilent SureSelect bed files

[Kath]

Hello,

Can anyone tell me what the difference is between these bed files supplied by Agilent for their SureSelect Human All Exon V2 kit:

_Regions.bed
_Padded.bde
_Covered.bed
_AllTargets.bed

Thanks!

[Bukowski]

The padded bed file is the regions that are baited, with an extension of 50 bases to either end. Where this regions meet they are merged into a single region.

These tend to extend into the intronic regions (and generally defines what you can confidently genotype).

Regions is the regions the kit is designed to (I think). Covered is the regions that are baited for capture.

[Elsie]

Very helpful, thanks.