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AdmiralenOla / Scoary

Pan-genome wide association studies
GNU General Public License v3.0
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VCF GWAS #76

Closed ahmedmagds closed 3 years ago

ahmedmagds commented 5 years ago

How do I use multiple vcf files to create the Scoary csv to be used with the the main script? Or in other words if I start with multiple vcf files of different isolates mapped to the same reference, how can I get scoary results (similar to starting from roary).

AdmiralenOla commented 3 years ago

Hi @ahmedmagds,

Replying way too late to your question. Sorry. You should be able to merge your VCF files using bcftools merge. You should then be able to run Scoary's vcf2scoary script on this merged VCF file. Note that this script is very much in beta version, and I'd appreciate bug reports. The file you get from vcf2scoary can be used instead of a gene_presence_absence.csv file from Roary. Note that you have to specify the correct start column (-s) when you run Scoary.

ahmedmagds commented 3 years ago

Thanks @AdmiralenOla !