Start from a list of dbSNP target identifiers

Use the following example of creating a BED file from dbSNP targets with the UCSC Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables) to generate BED files from other variant formats, such as ClinVar.

  1. In the UCSC Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables), make the following selections from the dropdown lists.

    Field

    Selection

    assembly

    Feb.2009 (GRCh37/hg19)

    group

    Variation

    region

    genome

    output format

    BED - browser extensible data

    The track and table sections are populated with available SNP databases from dbSNP.

  2. In identifiers (names/accessions) section, click either paste list or upload list.

    Depending on your selection, Paste in Identifiers or Upload Identifiers screen opens.

  3. Either upload a text file listing your dbSNP identifiers by clicking Choose File, or paste the list into the provided field, then click submit.
  4. Click get output.

    The Output as BED screen opens.

  5. In the Create one BED record per: section, select padding with Whole Gene, Upstream, or Downstream options. If needed, adjust the padding value.
  6. Click get BED.

    The BED file has the following format, or similar.

Upload the BED-formatted file to Ion AmpliSeq™ Designer.

Related Topics
Parent topic: Create a BED file from a list of variants