Requirements for GRCh38 custom BED file

If you create a custom BED file for a custom analysis that uses the GRCh38 reference, consider the following:

Public standard:

  • See the BED file specification as described by UCSC.

  • Annotation files contain three types of lines: browser lines, track lines and data lines.

  • Empty lines and those starting with '#' are ignored.

  • A track line begins with the word 'track', followed by one or more key=value pairs.

  • There are currently 16 key=value pairs recognized by UCSC, but other key=value pairs are allowed.

  • The key db=<UCSC_assembly_name> specifies the reference, but must be a valid UCSC assembly ID (e.g. hg19).

Example:

track name="CHP2_designed" description="Amplicon_Insert_CGP2" visibility=2 db=hg19

track name="CHP2_designed" description="Amplicon_Insert_CGP2" visibility=2 db=hg38

Recommendation:

Include the key=value pair db=<UCSC_assembly_name> as shown in the example.

Define an additional key=value pair in the format reference=hg19 or reference=GRCh38.p2 and include it on the track line.

For hg19, including the key=value pair reference=hg19 is optional.

If a URI is desired, define an additional key=value pair in the format referenceURI=http://www.thermofisher.com/GRCh38.p2.fasta .