B-allele frequencies plot

[thangnx1012]

Hi,
Thank you so much for developing the tools.
I have a question related to the Wakhan plot, and I could not see the B-allele frequencies in my final plot. Here is my code to run the plot
python wakhan.py --threads 50
--reference ${hg38_reference}
--target-bam ${longphase_clair3_outdir}/${samplename}_haplotagged.bam
--tumor-vcf ${clair3_outdir}/${samplename}/phased_merge_output.vcf.gz
--genome-name ${samplename}
--reference-name hg38
--contigs chr1-22,X,Y
--loh-enable
--pdf-enable
--out-dir-plots ${wakhan_outdir}/${samplename}
--breakpoints ${severus_outdir}/${samplename}/all_SVs/severus_all.vcf

Here is the plot generated from this code.
https://drive.google.com/drive/folders/1cuhhqe_gdA1r2SdgqQkaaZJpRZkPsHrY?usp=sharing
I do see the B-allele frequencies in each chromosome plot but not in the summary plot. Thank you

[tahashmi]

Hi @thangnx1012 , actually you have to enable b-allele freq by clicking on BAF legend in main plots (these are disabled by default for visualization as it can take some extra memory in browser). Similarly what you see in red/blue dots are haplotype specific coverage bins. I will update the doc soon.

[thangnx1012]

Oh, great! I did!
Thanks for the quick reply. I only look at the PDF file, so I don't think about that option in the HTML file.