Variation consequences

This presentation shows how you can use the Ensembl APIs to find out how variants affect genes and transcripts, including SO consequence terms.

Exercise 4a

1. Fetch all transcript variations (germline and somatic) in transcript ENST00000001008 in human and retrieve the following information:
   • Variation name
   • Consequence type (most severe)
   • Amino acid change*
   • Position in cDNA* and position in translation*
     * if information is available
     
2. In a second attempt filter for transcript variations of consequence type: ‘missense_variant’
   
   Hint: fetch_all_by_Transcripts method requires a listref of objects; so use e.g. [$transcript] instead of $transcript

Anja explains the answers to these questions in this 4-minute video. You can also download her sample script and expected output.