Server Input
PhD-SNPg server takes in input a list of variants in three different formats. Two formats (CSV and VCF) require the genomic location of the variants and the nucleotide change. The MUT format, which requires a list of amino acid changes, allows to map the residue substitution to the corresponding nucleotide variants. The three input formats are summarized as follows:
CSV: The simplest input format uses comma separated values which indicates the chromosome (chr), the position (pos), the reference (ref) and alternative (alt) alleles as follows: chr,pos,ref,alt (see example 1).
VCF: The variants can be also provided in a VCF like format that requires at least 5 columns (chr,pos,id,ref,alt) separated by spaces. When the id is not available, it can be replaced by a dot character (see example 2).
MUT: The effect of single amino acid variants can be predicted providing in input the 2 columns including the gene symbol and the mutation (gene,mutation) separated by comma (see example 3).
For all the input formats, each variant is provided in a separated row of the textarea box.
In addition, all the input variants can be uploaded as a single file in text or zipped format. For formatting
reasons, it is recommended to avoid the cutting and paste of VCF input data which can be easily upload as
zip file. Before the submission of the process please select the appropriate assembly of the human genome on
which the genomic location are expressed.
To prevent the submission of large processes, a maximum number of 1,000 variants for each job is allowed. For
predicting the impact of a larger of variants, please install PhD-SNPg on your local machine.
The information for the local installation of PhD-SNPg are reported in method page.