Closed HamletShaoE closed 8 years ago
Hello, HamletShaoE! As suggested by our recent paper in Bioinformatics, we are in the process of incorporating VCF, and hope to have this accomplished in about a week's time. Thanks for your feedback, and we hope to have this addressed very soon! Best wishes.
There are essentially two kinds of VCF files we are trying to incorporate. The first is a VCF file which summarizes multiple individual sequencing experiments. In such a case, in the "INFO" column, there is typically an "NS=" (number of samples), and an "AF=" (allele frequency) entry. On the other hand, we also have people who have performed single-run pooled-sequencing experiments, in which case there's usually a "DP4=" entry in the "INFO" column, containing the number of reference and allele forward and reverse reads. Do your data fit one of these situations? I not, I'll want to make sure that your situation is included.
The latest SNPGenie incorporates two versions of VCF. Please let us know if your format differs from these by opening a new Issue.
Hi, I notice that snpgenie takes CLC or Geneious format for input, how about take vcf format into consideration, since human and fly have well data in this format. thanks