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Release Notes for Oncotator version 1.3.0

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
edited July 2014 in Oncotator documentation

Oncotator version 1.3.0 was released on July 24, 2014. This document lists the main changes that were made to the program. For more details about code changes, please see the source code on Github.


Addition of a new input format (SEG_FILE) and new output format (GENE_LIST)

The new format options are as follows:

  • SEG_FILE is a list of segments to annotate
  • GENE_LIST will produce a list of genes and the segment annotations.

GENE_LIST will produce results for different exons if a segment endpoint falls in a gene. If a segment endpoint falls in an exon, the exon is included. For example, "6+" indicates "exon 6 (0-based) and above are included in the segment".

Only the ENSEMBL (GENCODE) datasource annotates segments

Annotations included are:

  • genes -- a list of genes in the segment
  • start_gene -- the gene overlapping the start of a segment. Will be "" if start is IGR
  • start_exon -- index of the exon overlapped by the start of the segment and whether all upstream or downstream exons (in the coding direction). 0-based indexing. For example, "6-" for a segment on a negative strand transcript with start overlapping the 6th exon (0-based indexing)
  • end_gene -- the gene overlapping the end of a segment. Will be "" if end is IGR
  • end_exon -- index of the exon overlapped by the end of the segment and whether all upstream or downstream exons (in the coding direction) overlap the segment. For example, "6+" for a segment on a negative strand transcript with end overlapping the 6th exon (0-based indexing)

If the input is SEG_FILE, only output formats of SIMPLE_TSV and GENE_LIST are supported.

Known issues:

  • VCF is not supported yet (see issue #204 on Github).
  • Cytoband annotation is not implemented yet.
Post edited by LeeTL1220 on

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