Transcript identifier (Ensembl or RefSeq) or name of the gene (HUGO symbol) plus the aminoacid change following HGVS format.
The longitude of the frameshift (till the new reading frame ends in a stop codon) needs to be stated to retrieve the corresponding nucleotide change, which is used to calculate certain metrics used by the CGI; if not available, APC:p.I1557fs is also allowed)
If you upload a file, the protein change column needs to be labeled as protein in the header. The sample identifier can be also included in a column labeled sample separated using a <tab> character. Any other column will be ignored but included in the output.
The chromosome, genome position and reference/alternative alleles (annotated in the positive strand) following HGVS format.
If you upload a file, the nucleotide change column needs to be labeled as gdna in the header. The sample identifier can be also included in a column labeled sample separated using a <tab> character. Any other column will be ignored but included in the output. Only hg19 annotation is currenlty supported.
The chromosome, genomic position and reference/alternative alleles (annotated in the positive strand) separated in different columns.
If you upload a file, the columns need to be labeled as chr, pos, ref and alt and separated using a <tab> character. The sample identifier can be also included in a column labeled sample. Any other column will be ignored but included in the output. Only hg19 annotation is currenlty supported.
The VCF format is accepted only if you upload a file. Check the format details in this link
Only hg19 annotation is currenlty supported.
The gene plus the alteration type separated by the colon character.
If you upload a file, this information needs to be stated in two different columns labeled as gene and cna in the header, respectively, separated using a <tab> character. The valid entries for the cna column are etiher amp or del (case insensitive). The sample identifier can be also included in a column labeled sample. Any other column will be ignored but included in the output.
Translocations are stated by the two partners separated with the '__' character (two underscores). The translocations are processed regardless of the order of the partners.
If you upload a file, the fusion partners column need to be labeled as fus in the header of a tab-separated file. The sample identifier can be also included in a column labeled sample. Any other column will be ignored but included in the output.