How can I draw this plot?

Question

[mohammadhassanj]

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

Source : https://samtools.github.io/bcftools/howtos/roh-calling.html

[bernatgel]

Hi mohammadhassanj,

I don't know exactly the format of the files produced by this command, but if you can use R, I'm pretty sure you can plot them using karyoploteR and maybe with the help of CopyNumberPlots to easily get the variant allele frequencies from the VCF. You can check the karyoploteR tutorial to find some more information and examples.

[mohammadhassanj]

ST  [2]Sample   [3]Chromosome   [4]Position [5]State (0:HW, 1:AZ)   [6]Quality (fwd-bwd phred score)

ST  Sample1 chr1    14907   0   3.0
ST  Sample1 chr1    14930   0   95.5
ST  Sample1 chr1    15118   0   99.0
ST  Sample1 chr1    15211   0   99.0
ST  Sample1 chr1    15274   0   90.8
ST  Sample1 chr1    15820   0   90.0
ST  Sample1 chr1    16378   0   99.0

Hi bernatgel

thanks for reply

According to the command, a file is generated in above format in which the roh is estimated, but I do not know how to calculate "heterozygosity as dosag". Thank you

[gubrins]

Heys, did you manage to plot it?

[taniamahmood38]

If you have found any tool to visualize it, then kindly let me know

[gubrins]

Heys, what I did is to filter out the RG observations from the first column and then plot them along the genome with R. I did not manage to obtain this plot.

[taniamahmood38]

Hey, kindly help if you have found any tool to visualize it ?