Transcript set

You can use a transcript set in Ion Reporter™ Software to provide annotation information for specific transcripts of interest. A transcript set limits the annotations that are applied to your variant calls to annotations that match your list of preferred transcripts.

Use the following guidelines when you use or create a transcript set:

• Ensure that the transcript set includes a header line that indicates the human genome on which it is based. If this reference header information is not included, the software processes the file as if it is based on the hg19 human genome reference. The options for the header line are:

  • ##reference=GRCh38

  • ##reference=hg19

• The contents of the file for the transcript set are in the format: GENE_NAME transcript_accession_id1, transcript_accession_id2, ..., with a tab character between the gene name and the first transcript id.

• Gene names must be specified as HGNC gene symbols.

• A tab character is required after the gene name.

• A comma and a space character are required between transcripts.

• If gene name is missing in the file, all transcript annotations for that gene are preserved.

• Transcripts can be specified as RefSeq or Ensembl® accession ids that include a version. However, if the accession id contains no decimal point version, then all versions of the transcript are matched. For example, Gene1 NM_0000006 is matched with all versions of this transcript. This annotation source uses a TXT format with tab characters. In Ion Reporter™ Software 5.4 and later, the variant is annotated if the transcript names match, even if the version numbers of the custom transcripts do not match.

Here is an example file with a header to indicate that the transcript set is based on the GRCh38 human genome reference:

##reference=GRCh38
GENE REFSEQ_AND_ENSEMBL_TRANSCRIPTS
Gene1 NM_00000006.2, NM_000000005.3, ENST000000000007.3
Gene2 NM_00000001.1, NM_000000007.1, NM_0000000004.5,
NM_000000008.3, ENST000000000006.4
GENE REFSEQ_AND_ENSEMBL_TRANSCRIPTS
Gene1 NM_00000006.2, NM_000000005.3, ENST000000000007.3
Gene2 NM_00000001.1, NM_000000007.1, NM_0000000004.5, NM_000000008.3, ENST000000000006.4