Padding Coordinates or Creating a BED File from a List of Variants

Creating a BED File for Input to the Designer

You can generate a custom BED file with your target regions of interest from the UCSC Table Browser.

To create a BED-formatted file starting from a list of either COSMIC mutations or dbSNP identifiers, use the UCSC Table Browser of the UCSC Genome Browser. Make sure to select genome and assembly as Human, (GRCh37/hg19).

Working from a list of COSMIC ids

Table Browser

Select ‘All Tracks’ in the group drop-down list, and COSMIC for the track. Choose the cosmic option in the table list.

Starting from a list of dbSNP target identifiers

Table Browser with dbSNP selected

Select the “Variation and Repeats” group in the drop-down menu. The track and table sections are then populated with available SNP databases from dbSNP.

Choose the genome radio button for the region selection. Click on either the paste list or upload list button next to identifiers.

Identifier selection

Either upload a text file listing your COSMIC or dbSNP ids or simply paste in the list and click submit. For the output format, select BED – browser extensible data.

Format selection

After clicking on the get output button, the Output as BED screen allows for padding with Whole Gene, Upstream or Downstream.

BED options

The BED file will be similar to the following format:

BED format selected

This BED-formatted file can be uploaded to the Ion AmpliSeq Designer.

Use the UCSC Genome Browser to Create a BED file with Padded Exons

Using the Table Browser, select the following options:

  • Group: Genes and Gene Prediction Tracks
  • Track: RefSeq Genes
  • Table: refGene
  • Output format: BED – browser extensible data

Table browser

Upload or paste a list of gene identifiers. When you click submit, you will be directed to the Output refGene as BED page. Select options to add upstream or downstream base padding, or bases at each end of the exons. Additionally, select to create the BED file to include 5’ or 3’ UTR Exons or CDS.

Output options