I am trying to do a test GWAS using SNPs for 12 strains of Gallibacterium, fitting different antibiotic resistance binary vectors. If I understand correctly, Scoary can also take SNP presence/absence tables as input. I have generated the SNP file with parsnp in vcf format, but the vcf2scoary failed to convert it. Could be possible to have an example of how the input format should be formatted for SNPs? So that I could produce it with a custom script if it is not too difficult. Alternatively, would it be possible to update the vc2scoary script if it is not too much work?
parsnp.vcf.txt
Dear Author,
I am trying to do a test GWAS using SNPs for 12 strains of Gallibacterium, fitting different antibiotic resistance binary vectors. If I understand correctly, Scoary can also take SNP presence/absence tables as input. I have generated the SNP file with parsnp in vcf format, but the vcf2scoary failed to convert it. Could be possible to have an example of how the input format should be formatted for SNPs? So that I could produce it with a custom script if it is not too difficult. Alternatively, would it be possible to update the vc2scoary script if it is not too much work?
Thank you!
Kind regards Nicola