I imported the VCF file and combined FIX and INFO to create a data frame. This data frame contains VCF file information such as CHROM, POS, REF, ALT, QUAL, FILTER, etc. I want to draw a manhattan plot with this data frame. The problem is that p-value is needed to draw the manhattan plot. With this information I have, how can I find the p-value and draw a manhattan plot?
The image above is an image that only retrieves the CHROM, POS, REF, ALT, and QUAL information for the data frame I have.
How can I find the p-value and get the manhattan plot?
Please help me.