plotting roh from bcftools

plotting roh from bcftools



I am following this small tutorial on how to calculate ROHs from a vcf file using bcftools ( and I am getting this txt file:

# This file was produced by: bcftools roh(1.10.2+htslib-1.10.2-3)
# The command line was: bcftools roh -G30 --AF-dflt 0.4 my_file.vcf
# RG    [2]Sample   [3]Chromosome   [4]Start    [5]End  [6]Length (bp)  [7]Number of markers    [8]Quality (average fwd-bwd phred score)
# ST    [2]Sample   [3]Chromosome   [4]Position [5]State (0:HW, 1:AZ)   [6]Quality (fwd-bwd phred score)
ST  Leopards_1  NC_018723.3 280 0   3.0
ST  Leopards_1  NC_018723.3 281 0   27.7
ST  Leopards_1  NC_018723.3 292 0   27.7
ST  Leopards_1  NC_018723.3 293 0   27.7
ST  Leopards_1  NC_018723.3 303 0   27.7

I am wondering how to interpret the results and how to plot them. From the plot they show I don’t understand which are the ROHs areas and if there is a difference between ST and RG.
Any type of help would be more than appreaciated!





Read more here: Source link