I'm shamsur. I got this snp file of a goat breed. SNP file showes CHROM, POS, ID, REF, ALT, QUAL, FILTER AND INFO. Click the link 1 I have taken screenshot from my terminal as it was easy to open from terminal. I want to make a Manhattan plot using this snp file to visualize significant snp for gwas study. But Manhattan plot require p-value for plotting.
How I'm suppose to have this p-value?
Thanks in advance.
Based on the field names, your file fits the VCF (Variant Call Format) specification. Can you explain how this file was produced?
Yes, you need p-values in order to generate a Manhattan plot, and these p-values typically represent loci scatterred across the genome. Typically, we would generate such a plot using p-values from a comparison between groups, e.g., Asthmatic Adults versus Healthy Control Adults. However, as you have not explained anything about your experiment, we have no way to know where to look for these p-vales. They may be encoded in the VCF. Please paste some lines from the VCF.