Hi,

I have to plot allele frequencies of two different SNP chip datasets. I have two VCF files and would like to make a scatterplot in which these 2 datasets are plotted one against each other. What is the easiest way to do this?
I apologize if this question was already posted.
    bcftools query -i 'N_ALT=1' -f '%CHROM\_%POS\_%REF\_%ALT\t%INFO/AF\n' in1.vcf.gz | sort -t $'\t' -k1,1 > a.tsv
    bcftools query -i 'N_ALT=1' -f '%CHROM\_%POS\_%REF\_%ALT\t%INFO/AF\n' in2.vcf.gz | sort -t $'\t' -k1,1 > b.tsv
    join -a 1 -a 2  -o '1.2,2.2'  -t $'\t' -1 1 -2 1 -e 0.0 a.tsv b.tsv > compare.tsv

plot with R : https://stackoverflow.com/questions/42232340/how-to-read-tab-separated-files-in-r-to-generate-scatterplot
