How to convert VCF into hapmatrix format?

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23 months ago

taniamahmood38 ▴ 50

Dear everybody,

I have a vcf file and I am using sfsR function of popseq package on R software. The link to package is http://rdrr.io/github/sdwfrost/popseq/man/sfsR.html#heading-5

It requires hapmatrix as input and I have no idea of hapmatrix file structure. Can anyone please help me how to convert my vcf into hapmatrix? By using which tool and what is its command? Any help would be highly appreciated.

Thanks in advance

popseq hapmatrix vcf • 683 views

ADD COMMENT • link 23 months ago by taniamahmood38 ▴ 50

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How did you pick this package? Are you following a workflow outlines somewhere?

ADD REPLY • link 23 months ago by Ram 43k

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I found this package on github http://github.com/sdwfrost/popseq and then I installed this package on R. No, I am not following any outline as such.

ADD REPLY • link 23 months ago by taniamahmood38 ▴ 50

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Installing random packages is not something you should be doing at this level - it is a more advanced challenge for once you're familiar with how to substitute parts of existing pipelines with your own plug and play modules.

Never a bad time to get started though, so congrats. Try to understand the haplotype matrix format and look for tools that can get you from VCF (or maybe a different upstream format) to that format. It might be a simple awk command once you understand the hapmatrix format well. Look at the information content in both formats and see if they're compatible.