Using PIGx starting from VCF files

[Kremsky, Isaac]

Hi,

I am working with SARS-Cov2 data from wastewater samples and would like to use your pipeline on it, as it produces nice plots and is designed for wastewater samples like we have.  However, the sequencing company we used will only provide us with the .vcf files and not with the raw fastq files.  I was wondering which scripts I could use starting with my VCF files, to produce SNP frequency plots like are on your website?  That may also be a nice feature to add into your software at some point, but if you could just tell me which scripts to use and the order to use them, that would be great for now.

Thanks!

Isaac Kremsky, Ph.D.

Assistant Professor

LOMA LINDA UNIVERSITY HEALTH | School of Medicine

Department of Basic Sciences

Chan Shun Pavilion, Room A1022

11175 Campus St.

Loma Linda, CA  92354

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