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pgSnp to gd_snp (version 1.0.0)

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.