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Circos plot using vcf : Mutect2 MultiSample VCF out file

Hi

I have multisample vcf out file from Mutect2 and would like to make circos plot showing variants in multiple sample.

Any suggestions or directions please ?

mutect2 vcf
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updated by alwayshope • alwayshope • written by m. bioinfo • m. bioinfo

what kind of graphics do you want and what did you try so far ?

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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks for reply! My expectations are to create such a figure using my multisample vcf file which is a MuTect2 output. First choice of image is published here link Other images are from published articles and mentioned online at circos webpage.

I have tried circos examples and able to create for fusions only on single sample.

Would you have something to suggest or direct me ?

enter image description here

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updated by Pierre Lindenbaum Pierre Lindenbaum • written by m. bioinfo • m. bioinfo

1 answer

If you want to create one track per sample, the idea is to loop over the samples and to create a file for each samples. Something like (not tested)

bcftools query -l in.vcf.gz | while read S
do
  bcftools view --samples "${S}" in.vcf.gz | bcftools query -f '[%CHROM\t%POS0\t%END\t%SAMPLE\t%GT\n] | grep -v '0/0$'  > "${S}.bed"

done
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written by Pierre Lindenbaum Pierre Lindenbaum

thanks Pierre ! and I suspect this .bed output should be used as input for Circos. Do I need any corrections here ? 😊

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written by m. bioinfo • m. bioinfo

May I know if you solved this? Thanks a lot!

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written by alwayshope • alwayshope

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