Separate pgSnp alleles

Dataset formats

The input dataset is of Galaxy datatype interval with the columns specified for pgSnp. Any additional columns beyond the pgSnp defined columns will be appended to the output. The output dataset is in interval format. (Dataset missing?)

What it does

This separates the alleles from a pgSnp dataset into separate columns, as well as the frequencies and scores that go with the alleles. It will skip any positions with more than 2 alleles. If only a single allele is given then "N" will be used for the second, with a frequency and score of zero. Or, if a column with reference alleles is provided, the value in that column will be used in place of the "N" for single alleles.

Examples

• input pgSnp file:

  chr1    256     257     A/C     2       3,4     10,20
  chr1    56100   56101   A       1       5       30
  chr1    77052   77053   A/G     2       6,7     40,50
  chr1    110904  110905  A       1       8       60
  etc.
  

• output:

  chr1    256     257     A       3       10       C       4       20
  chr1    56100   56101   A       5       30       N       0       0
  chr1    77052   77053   A       6       40       G       7       50
  chr1    110904  110905  A       8       60       N       0       0
  etc.