Dataset formats

The input dataset is of Galaxy datatype interval, with the additional columns required for pgSnp format. Any further columns beyond those defined for pgSnp will be ignored. The output dataset is a gd_snp table. (Dataset missing?)

What it does

This tool converts a pgSnp dataset to gd_snp format, either starting a new dataset or appending to an old one. When appending, if any new SNPs appear only in the pgSnp file they can either be skipped entirely, or backfilled with "-1" (meaning "unknown") for previous individuals/groups in the input gd_snp dataset. If any new SNPs are being added (either by creating a new table or by backfilling), then an extra column with the reference allele must be supplied in the pgSnp dataset, as shown in the example below.

Example

• input pgSnp file, with reference allele added:

  chr1    1888681  1888682  C/T     2       4,3     0.8893,0.8453   T
  chr1    3118325  3118326  T       1       8       0.8796          C
  chr1    3211457  3211458  A/C     2       17,10   0.8610,0.8576   A
  etc.
  

• gd_snp output:

  chr1    1888681   T       C      -1      3       4       1     0.8893
  chr1    3118325   C       T      -1      0       8       0     0.8796
  chr1    3211457   A       C      -1      17      10      1     0.8576
  etc.