plotting roh from bcftools
I am following this small tutorial on how to calculate ROHs from a vcf file using bcftools (samtools.github.io/bcftools/howtos/roh-calling.html) 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 Sample Chromosome Start End Length (bp) Number of markers Quality (average fwd-bwd phred score) # ST Sample Chromosome Position State (0:HW, 1:AZ) 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!
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