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gene_annotation2bed

Custom script for processing a list of ids (HGNC, transcript) or coordinates with associated annotation, into a comprehensive bed file for the corresponding refseq transcripts for each ID entry.

What are typical use cases for this app?

  • Converting a list of HGNC ids + associated gene level annotation information into a comprehensive bed file for annotation with Ensemble's VEP.
  • Other use cases include providing different inputs such a list of transcripts/exact coordinates.

What data are required for this app to run?

  • List of ids and annotation information in TSV format.
  • Human Genome Reference (i.e. hs37d5)
  • RefSeq Transcripts file (gff3)

IGV reports output

Example Output: [!image] (https://raw.githubusercontent.com/eastgenomics/gene_annotation2bed/dev/data/demo/demo_igv_reports.png)

The script produces a HTML report of all the bed file entries. Displayed in IGV with the refseq track and bed file aligned with the respecive annotation.

Script Inputs - Defaults & Behaviour

  • Genome (required): The genome build for the resource
  • Refseq gff (--gff_file): The corresponding gff file for refseq transcripts for the genome build.
  • OR the processed dataframe for the refseq gff in pickle format (--pickle).
  • annotation or transcript file with the annotation information in TSV format.
  • The reference fasta for using for igv reports (i.e. -fasta hs37d5.fa.gz), the corresponding index should be present in the same folder.
  • The output file suffix for the outputed .bed file.
  • Flanking (int): The required flanking either side of the transcripts selected.
  • Assembly summary - corresponding assembly report file for the refseq.gff, this is used to determine the corresponding chromosome for each transcript.

Requirements

  • pysam
  • pandas
  • igv-reports (v) argparse
  • numpy
  • re

install using requirements.txt. pip install requirements.txt