BED/GFF Input

Bvalcalc estimates the effects of BGS on linked (and unlinked) sites due to direct purifying selection in conserved regions of the genome.

When using the --region and genome modules, all annotated regions in the BED/GFF/CSV annotation file will be used to estimate calculate BGS effects

--bedgff [path/to/example.bed]

Path to an annotation file of selected elements, in BED, GFF3 or CSV format (CHR,START,END). Header information, indicated by #, is ignored.

Annotations

The annotations indicated in the BED/GFF/CSV input will all be assumed to have the same distribution of fitness effects (DFE), though this may not always be the case.

Typical annotations that are expected to experience purifying selection are exons and regulatory regions. Inferred conserved elements such as phastCons or GERP elements can make for excellent inputs for Bvalcalc.

If you have DFE information for the different annotation types (e.g., CDS and UTRs), consider running Bvalcalc separately for each and combining the results, see Multiple DFEs.

Example

Three example inputs to --bedgff that will be processed identically:

#GFF3 format
2R  .       .       326768  705848  .       .       .       .
2R  .       .       854814  855571  .       .       .       .
2R  .       .       924636  951252  .       .       .       .

#BED format
2R  326768  705848
2R  854814  855571
2R  924636  951252

#CSV format
2R,326768,705848
2R,854814,855571
2R,924636,951252