VCF file comparison and plotting them

Question

[Sara]

I have 2 vcf files and want to compare them and make some plots including venndiagram. I tried bcftools to compare 2 vcf files but it does not make any plot. Do you know what tool I can use for this purpose?

[Ram]

Use bcftools to perform the intersect operation then R to summarize and plot.

Answer 1

[Pierre Lindenbaum]

A one liner:

comm \
   <(bcftools query -f '%CHROM:%POS:%REF:%ALT\n' vcf1.vcf.gz |  sort )  \
   <(bcftools query -f '%CHROM:%POS:%REF:%ALT\n' vcf2.vcf.gz |  sort )  |\
    awk -F '\t' '{if($1!="") N1++; if($2!="") N2++;if($3!="") N3++;} END {printf("pdf(\"out.pdf\");barplot(c(%d,%d,%d),main=\"compare\",ylab=\"Variants\",names.arg=c(\"uniq to VCF1\",\"uniq to VCF2\",\"Common\"));dev.off();\n",N1,N2,N3);}' |\
   R --vanilla

[Ram]

Run it on a headless node and suffer! Maybe add a pdf() so the plot is written to file?

[Pierre Lindenbaum]

Run it on a headless node and suffer!

fixed