bcftools How can I draw this plot?

I used the following command on the vcf file to calculate roh. My question is how can I have this plot?

bcftools roh -G30 --AF-dflt 0.4 file.vcf

plot source : https://samtools.github.io/bcftools/howtos/roh-calling/roh-example.png

Apr 27 '21 05:04 pythonlo7er

This plot was produced manually using matplotlib. BCFtools currently does not provide a tool to generate it. There is a plan to produce interactive graphs like this, but this work (https://github.com/GenciJakub/BcThesis) has not been ported to BCFtools yet and is not production ready.

May 24 '21 10:05 pd3

Hi, I'm also interested in plotting the results, how do you recommend to do it or at least could you provide the code you used to produce the file that @pythonlo7er mentioned?

Thanks in advance

Sep 17 '21 14:09 gubrins

Heys again,

If i understod properly, what I do to plot the results from bcftools is: first, filter the output to just keep the elements containing RG in the first column. Then, with chromomap you can plot it, giving a reference genome before hand (https://cran.r-project.org/web/packages/chromoMap/vignettes/chromoMap.html#My_first_chromoMap).

Let me know if you found any other way!

Oct 27 '21 09:10 gubrins