DiscoSNP++ VCF file REF field

Question

[tkitapci]

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

Answer 1

[pierre.peterlongo]

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