Multiple DFEs

Different annotated genomic elements that are expected to be under evolutionary constraint (e.g. CDS, UTRs, promoters, enhancers etc.) will have different distributions of fitness of effects (DFEs).

To account for different DFEs that may affect different annotated regions, you can run Bvalcalc for each DFE iteratively with the help of the --prior_Bmap flag in the --genome mode.

Arguments

--prior_Bmap [path/to/prior_Bmap.csv]

Optional prior B-value map (.csv format). Used to multiply the newly calculated B-values by a per-site prior (e.g. for regions under different selection parameters).

Format: Chromosome,Position,Conserved,B. Note that Conserved is required for parsing but does not affect output

Example Walkthrough

Let’s briefly walk through how you would generate a B-map that considers the combined effects of CDS (strongly deleterious DFE) and UTRs (moderately deleterious DFE).

1. Save a local a template params file using --generate_params for each of your annotations (CDS and UTR). See Generate Parameters

Bvalcalc --generate_params drosophila
scp DrosophilaParams.py CdsParams.py
scp CdsParams.py UtrParams.py

2. Tailor the CdsParams.py/UtrParams.py files with the respective DFEs. See Tailoring Parameters

3. Run --genome to create a B-map considering only the first annotation type (e.g. CDS). See Calculate Genome B-map

Bvalcalc --genome \
    --pop_params CdsParams.py \
    --bedgff_path drosophila_CDS.bed \
    --out CDS_B.csv \
    --out_binsize 1000

4. Run --genome and pass in the first annotations (CDS) Bmap --prior_Bmap as an additional argument.

Bvalcalc --genome \
    --pop_params UtrParams.py \
    --bedgff_path drosophila_UTR.bed \
    --prior_Bmap CDS_B.csv \
    --out UTR_CDS_B.csv \
    --out_binsize 1000

We now have a B-map (UTR_CDS_B.csv) that considers the effects of both CDS and UTRs.