Circos plot using vcf : Mutect2 MultiSample VCF out file

Question

[m. bioinfo]

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 ?

[Pierre Lindenbaum]

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

[m. bioinfo]

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 ?

Answer 1

[Pierre Lindenbaum]

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

[m. bioinfo]

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

[alwayshope]

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