gencode

Gencode parser for vdftools. Current version v47 (GRCh38), produces:

data/transcripts.parquet

• transcript_chrom (string)
• transcript_start (integer)
• transcript_end (integer)
• transcript_id (string) # ENST
• gene_id (string) # ENSG
• gene_symbol (string)
• is_coding (bool)
• is_pos_strand (bool)
• is_seleno (bool) # is selenoprotein
• priority_level (integer)
• exon_total (integer) # exon count
• is_excludable (bool) # transcripts with problems (ie. readthrough, no-start, no-end)

Priority Levels:

1. APPRIS alternative 2

2. APPRIS alternative 1

3. APPRIS principal 5

4. APPRIS principal 4

5. APPRIS principal 3

6. APPRIS principal 2

7. APPRIS principal 1

8. MANE Clinical

9. MANE Select

data/exons.parquet

• exon_chrom (string)
• exon_start (integer)
• exon_end (integer)
• transcript_id (string) # ENST
• exon_number (integer)
• bases_preceding_exon (integer) # total bases in preceding exons

data/cds.parquet

• cds_chrom (string)
• cds_start (integer)
• cds_end (integer)
• transcript_id (string) # ENST

data/branch_sites.parquet

• branch_chrom (string)
• branch_start (integer)
• branch_end (integer)
• transcript_id (string) # ENST

data/transcript_sequences.parquet

• transcript_id (string) # ENST
• orf_start_pos_in_transcript (integer) # 0-based position of A in start codon
• orf_end_pos_in_transcript (integer) # closed position end of stop codon
• transcript_sequence (string) # ACGT, coding transcripts