Question

VCF file comparison and plotting them

0

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2.7 years ago

Sara ▴ 270

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?

vcf • 970 views

ADD COMMENT • link updated 2.7 years ago by Pierre Lindenbaum 164k • written 2.7 years ago by Sara ▴ 270

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

ADD REPLY • link 2.7 years ago by Ram 44k

score 2 · Answer 1 · 2022-04-06

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2.7 years ago

Pierre Lindenbaum 164k

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

ADD COMMENT • link 2.7 years ago by Pierre Lindenbaum 164k

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

ADD REPLY • link 2.7 years ago by Ram 44k

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Run it on a headless node and suffer!

fixed

ADD REPLY • link 2.7 years ago by Pierre Lindenbaum 164k