Bringing in files from the BX table browser

In the Tools panel on the left, click on the category called Get Data to open it. There are many options under Get Data for bringing in files or datasets into Galaxy. We are going to use the BX table browser a partial mirror of the UCSC Main table browser, as it specializes in personal genomes.

Click on BX table browser (red arrow) in the tool panel and the right panel will temporarily hide making more room in the middle panel for the Table Browser interface. First make sure the genome and assembly are correct; we want Human build hg19. We want the group Personal Genomes, track Genome Variants, and table CEU NA12878 (pgNA12878CG). Be sure to select the exact table name shown because 1000 Genomes also sequenced this individual as part of the CEU trio. We want to use the full set from Complete Genomics and not add further complications that may arise from different technologies or SNP calling methods. All of these options are in the red box below. We want the SNPs from the whole genome (red arrow). Though often the BED format is best for the output in this case we want the pgSnp (personal genome SNP) format, which is the format of this table. We want "all fields from selected table" and we want the results to go back to Galaxy (red arrows). Then click the "get output" button (green arrow). On the next page that comes up click the Send query to Galaxy button.