How to detect recombinant region of bacterial genome

Question

[jeccy.J]

Hi all I have to detect the recombinant region of several bacterial genome. I did all the alignment using Harvest suit and generate the VCF file for all the snps position. Can anyone suggest me how I can find the recombinant region from that data.

Thanks advance.

[zizigolu]

• https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html
• https://wiki.transmartfoundation.org/pages/viewpage.action?pageId=3047426
• http://vcftools.sourceforge.net/

in windows you might use CLC bio workbench