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DiscoSNP++ VCF file REF field

Hi,

In the VCF file generated there is the "REF" and "ALT" fields which stands for reference allele and alternative allele respectively. Since there is no reference sequence when running discoSNP++ what is the interpretation of the REF allele given in the VCF file?

Thanks

Best Regards
T. Hamdi Kitapci

vcf discosnp ref
• 1,898 views • link
updated by Ram Ram • written by tkitapci tkitapci

1 answer

Hi,

(from the vcf_creator documentation):

REF: If one of the two predicted allele maps this position: the corresponding variant. Else, or if no reference genome provided : the lexicographically smallest of the two variants In case of close SNPs : the first is defined as previously described. The following SNPs are those located on the same path
ALT: The variant non reported as the "REF" variant

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updated by Ram Ram • written by pierre.peterlongo pierre.peterlongo

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