Input for the VariantClassifier
The input into the VariantClassifier is very simple. It is a text file with 4 columns, each column is separated with a tab character.
1160 1161 1 G/T
2437 2438 1 G/C
4108 4109 1 C/G
20956 20957 1 C/T
28318 28319 1 G/A
The 1st column is the begin coordinate of your allele and the 2nd column is the end coordinate. Note that the begin/end coordinates must be in a local 0-space-based coordinate system. More information on coordinate systems.
The 3rd column is the orientation of your allele. 1 is on the forward strand. -1 is on the reverse strand.
The 4th column contains the alleles in the position. You may make one allele the reference and the second allele the mutant, or only specify one allele. These alleles may be SNPs, or variants of any length. Deletions should be represented with a hyphen, "-".
The length of a deletion will be computed by the VariantClassifier by looking at the begin/end coordinates you have specified in the first two columns. The length of the allele need not match the distance between begin/end coordinates. If the allele length is greater in length than the distance between begin/end coordinates, an insertion is assumed. If they are the same length, a substitution is assumed. If the allele length is shorter than the distance between begin/end coordinates, a deletion is assumed.