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Merged
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Mar 4, 2025
Merged

Allow vep annotation reporter to provide a list of preferred transcripts #81

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949429d
Allow vep annotation reporter to provide a list of preferred transcripts
susannasiebert Mar 3, 2025
a5474b7
Use PICK'ed value as a fallback when none of the preferred transcript…
susannasiebert Mar 4, 2025
9f72b39
Rename option
susannasiebert Mar 4, 2025
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77 changes: 77 additions & 0 deletions tests/test_data/vep_annotation_reporter/output.preferred_transcript.list.tsv
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Original file line number Diff line number Diff line change
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CHROM POS REF ALT transcript_id Consequence Gene Feature
chr17 7663110 G A ENST00000413465.6 intron_variant ENSG00000141510 ENST00000413465.6
chr17 7663126 GTATATATATAATATATATAATATAATATAA G ENST00000413465.6 intron_variant ENSG00000141510 ENST00000413465.6
chr17 7663661 A G ENST00000269305.8 downstream_gene_variant,intron_variant ENSG00000141510,ENSG00000141510 ENST00000269305.8,ENST00000413465.6
chr17 7666871 T C ENST00000269305.8 downstream_gene_variant,intron_variant ENSG00000141510,ENSG00000141510 ENST00000269305.8,ENST00000413465.6
chr17 7668134 G A ENST00000269305.8 downstream_gene_variant,intron_variant ENSG00000141510,ENSG00000141510 ENST00000269305.8,ENST00000413465.6
chr17 7668169 A AGCCGTG ENST00000269305.8 downstream_gene_variant,intron_variant ENSG00000141510,ENSG00000141510 ENST00000269305.8,ENST00000413465.6
chr17 7674797 T C ENST00000269305.8 intron_variant,intron_variant ENSG00000141510,ENSG00000141510 ENST00000269305.8,ENST00000413465.6
chr17 7675088 C T ENST00000269305.8 missense_variant,missense_variant ENSG00000141510,ENSG00000141510 ENST00000269305.8,ENST00000413465.6
chr17 7675327 C T ENST00000269305.8 intron_variant,intron_variant ENSG00000141510,ENSG00000141510 ENST00000269305.8,ENST00000413465.6
chr17 7675393 CTTT C ENST00000269305.8 intron_variant,intron_variant ENSG00000141510,ENSG00000141510 ENST00000269305.8,ENST00000413465.6
chr17 7675519 A G ENST00000269305.8 intron_variant,intron_variant ENSG00000141510,ENSG00000141510 ENST00000269305.8,ENST00000413465.6
chr17 7676154 G C ENST00000269305.8 missense_variant,missense_variant ENSG00000141510,ENSG00000141510 ENST00000269305.8,ENST00000413465.6
chr17 7676325 CCCCCAGCCCTCCAGGT C ENST00000269305.8 intron_variant,intron_variant ENSG00000141510,ENSG00000141510 ENST00000269305.8,ENST00000413465.6
chr17 7676483 G C ENST00000269305.8 intron_variant,intron_variant ENSG00000141510,ENSG00000141510 ENST00000269305.8,ENST00000413465.6
chr17 7684369 A G ENST00000269305.8 intron_variant ENSG00000141510 ENST00000269305.8
chr17 43047896 T C ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43049347 T C ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43057078 G A ENST00000471181.6 stop_gained ENSG00000012048 ENST00000471181.6
chr17 43058379 A C ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43059469 C CACAACA ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43059636 A G ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43063808 C T ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43064004 G A ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43066555 T C ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43067763 T C ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43067787 T C ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43071077 T C ENST00000471181.6 missense_variant ENSG00000012048 ENST00000471181.6
chr17 43074086 C T ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43074584 G C ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43074658 A T ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43077743 AT A ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43077746 T A ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43077756 T C ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43077760 G GT ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43077795 A G ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43077840 G A ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43077891 T A ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43079204 A C ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43079499 C T ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43082453 A G ENST00000471181.6 synonymous_variant ENSG00000012048 ENST00000471181.6
chr17 43087455 G A ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43087474 T C ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43091173 T G ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43091983 T C ENST00000471181.6 missense_variant ENSG00000012048 ENST00000471181.6
chr17 43092418 T C ENST00000471181.6 missense_variant ENSG00000012048 ENST00000471181.6
chr17 43092919 G A ENST00000471181.6 missense_variant ENSG00000012048 ENST00000471181.6
chr17 43093220 A G ENST00000471181.6 synonymous_variant ENSG00000012048 ENST00000471181.6
chr17 43093449 G A ENST00000471181.6 synonymous_variant ENSG00000012048 ENST00000471181.6
chr17 43093454 C T ENST00000471181.6 missense_variant ENSG00000012048 ENST00000471181.6
chr17 43097077 A G ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43097346 TA T ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43099629 T A ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43104083 AAAG A ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43121331 T C ENST00000471181.6 upstream_gene_variant,upstream_gene_variant,intron_variant ENSG00000198496,ENSG00000198496,ENSG00000012048 ENST00000356906.7,ENST00000467245.5,ENST00000471181.6
chr17 43121362 G C ENST00000471181.6 upstream_gene_variant,upstream_gene_variant,intron_variant ENSG00000198496,ENSG00000198496,ENSG00000012048 ENST00000356906.7,ENST00000467245.5,ENST00000471181.6
chr17 43127281 A G ENST00000471181.6 intron_variant&non_coding_transcript_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant,upstream_gene_variant ENSG00000198496,ENSG00000198496,ENSG00000012048,ENSG00000198496 ENST00000356906.7,ENST00000467245.5,ENST00000471181.6,ENST00000587322.1
chr17 43129737 G A ENST00000471181.6 intron_variant&non_coding_transcript_variant,intron_variant&non_coding_transcript_variant,upstream_gene_variant,upstream_gene_variant ENSG00000198496,ENSG00000198496,ENSG00000012048,ENSG00000198496 ENST00000356906.7,ENST00000467245.5,ENST00000471181.6,ENST00000587322.1
chr17 43131360 C T ENST00000587322.1 intron_variant&non_coding_transcript_variant,intron_variant&non_coding_transcript_variant,downstream_gene_variant ENSG00000198496,ENSG00000198496,ENSG00000198496 ENST00000356906.7,ENST00000467245.5,ENST00000587322.1
chr17 43131380 AAAT A ENST00000587322.1 intron_variant&non_coding_transcript_variant,intron_variant&non_coding_transcript_variant,downstream_gene_variant ENSG00000198496,ENSG00000198496,ENSG00000198496 ENST00000356906.7,ENST00000467245.5,ENST00000587322.1
chr17 43135863 A G ENST00000587322.1 intron_variant&non_coding_transcript_variant,intron_variant&non_coding_transcript_variant,downstream_gene_variant ENSG00000198496,ENSG00000198496,ENSG00000198496 ENST00000356906.7,ENST00000467245.5,ENST00000587322.1
chr17 43138596 G T ENST00000356906.7 intron_variant&non_coding_transcript_variant,intron_variant&non_coding_transcript_variant ENSG00000198496,ENSG00000198496 ENST00000356906.7,ENST00000467245.5
chr17 43138657 G C ENST00000356906.7 splice_region_variant&non_coding_transcript_exon_variant,splice_region_variant&non_coding_transcript_exon_variant ENSG00000198496,ENSG00000198496 ENST00000356906.7,ENST00000467245.5
chr17 43140410 C G ENST00000464237.2 downstream_gene_variant,upstream_gene_variant,intron_variant&non_coding_transcript_variant ENSG00000198496,ENSG00000267681,ENSG00000198496 ENST00000356906.7,ENST00000464237.2,ENST00000467245.5
chr17 43140722 G A ENST00000464237.2 downstream_gene_variant,upstream_gene_variant,intron_variant&non_coding_transcript_variant ENSG00000198496,ENSG00000267681,ENSG00000198496 ENST00000356906.7,ENST00000464237.2,ENST00000467245.5
chr17 43142914 TTG T ENST00000464237.2 downstream_gene_variant,upstream_gene_variant,intron_variant&non_coding_transcript_variant ENSG00000198496,ENSG00000267681,ENSG00000198496 ENST00000356906.7,ENST00000464237.2,ENST00000467245.5
chr17 43142940 G A ENST00000464237.2 downstream_gene_variant,upstream_gene_variant,intron_variant&non_coding_transcript_variant ENSG00000198496,ENSG00000267681,ENSG00000198496 ENST00000356906.7,ENST00000464237.2,ENST00000467245.5
chr17 43142964 GTGTATATATA G ENST00000464237.2 downstream_gene_variant,upstream_gene_variant,intron_variant&non_coding_transcript_variant ENSG00000198496,ENSG00000267681,ENSG00000198496 ENST00000356906.7,ENST00000464237.2,ENST00000467245.5
chr17 43145635 A C ENST00000464237.2 downstream_gene_variant,intron_variant&non_coding_transcript_variant ENSG00000267681,ENSG00000198496 ENST00000464237.2,ENST00000467245.5
chr17 43145975 G T ENST00000464237.2 downstream_gene_variant,intron_variant&non_coding_transcript_variant ENSG00000267681,ENSG00000198496 ENST00000464237.2,ENST00000467245.5
chr17 43146482 G A ENST00000464237.2 downstream_gene_variant,intron_variant&non_coding_transcript_variant ENSG00000267681,ENSG00000198496 ENST00000464237.2,ENST00000467245.5
chr17 43147572 C T ENST00000464237.2 downstream_gene_variant,intron_variant&non_coding_transcript_variant ENSG00000267681,ENSG00000198496 ENST00000464237.2,ENST00000467245.5
chr17 43147590 A G ENST00000464237.2 downstream_gene_variant,intron_variant&non_coding_transcript_variant ENSG00000267681,ENSG00000198496 ENST00000464237.2,ENST00000467245.5
chr17 43147814 C CCT ENST00000464237.2 downstream_gene_variant,intron_variant&non_coding_transcript_variant ENSG00000267681,ENSG00000198496 ENST00000464237.2,ENST00000467245.5
chr17 43147911 G C ENST00000464237.2 downstream_gene_variant,intron_variant&non_coding_transcript_variant ENSG00000267681,ENSG00000198496 ENST00000464237.2,ENST00000467245.5
chr17 43152446 T C ENST00000467245.5 intron_variant&non_coding_transcript_variant ENSG00000198496 ENST00000467245.5
chr17 43169893 C T ENST00000341165.10 upstream_gene_variant ENSG00000188554 ENST00000341165.10
77 changes: 77 additions & 0 deletions tests/test_data/vep_annotation_reporter/output.preferred_transcript.tsv
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Open in desktop
Original file line number Diff line number Diff line change
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CHROM POS REF ALT transcript_id Consequence Gene Feature
chr17 7663110 G A ENST00000413465.6 intron_variant ENSG00000141510 ENST00000413465.6
chr17 7663126 GTATATATATAATATATATAATATAATATAA G ENST00000413465.6 intron_variant ENSG00000141510 ENST00000413465.6
chr17 7663661 A G ENST00000269305.8 downstream_gene_variant ENSG00000141510 ENST00000269305.8
chr17 7666871 T C ENST00000269305.8 downstream_gene_variant ENSG00000141510 ENST00000269305.8
chr17 7668134 G A ENST00000269305.8 downstream_gene_variant ENSG00000141510 ENST00000269305.8
chr17 7668169 A AGCCGTG ENST00000269305.8 downstream_gene_variant ENSG00000141510 ENST00000269305.8
chr17 7674797 T C ENST00000269305.8 intron_variant ENSG00000141510 ENST00000269305.8
chr17 7675088 C T ENST00000269305.8 missense_variant ENSG00000141510 ENST00000269305.8
chr17 7675327 C T ENST00000269305.8 intron_variant ENSG00000141510 ENST00000269305.8
chr17 7675393 CTTT C ENST00000269305.8 intron_variant ENSG00000141510 ENST00000269305.8
chr17 7675519 A G ENST00000269305.8 intron_variant ENSG00000141510 ENST00000269305.8
chr17 7676154 G C ENST00000269305.8 missense_variant ENSG00000141510 ENST00000269305.8
chr17 7676325 CCCCCAGCCCTCCAGGT C ENST00000269305.8 intron_variant ENSG00000141510 ENST00000269305.8
chr17 7676483 G C ENST00000269305.8 intron_variant ENSG00000141510 ENST00000269305.8
chr17 7684369 A G ENST00000269305.8 intron_variant ENSG00000141510 ENST00000269305.8
chr17 43047896 T C ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43049347 T C ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43057078 G A ENST00000471181.6 stop_gained ENSG00000012048 ENST00000471181.6
chr17 43058379 A C ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43059469 C CACAACA ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43059636 A G ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43063808 C T ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43064004 G A ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43066555 T C ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43067763 T C ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43067787 T C ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43071077 T C ENST00000471181.6 missense_variant ENSG00000012048 ENST00000471181.6
chr17 43074086 C T ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43074584 G C ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43074658 A T ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43077743 AT A ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43077746 T A ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43077756 T C ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43077760 G GT ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43077795 A G ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43077840 G A ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43077891 T A ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43079204 A C ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43079499 C T ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43082453 A G ENST00000471181.6 synonymous_variant ENSG00000012048 ENST00000471181.6
chr17 43087455 G A ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43087474 T C ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43091173 T G ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43091983 T C ENST00000471181.6 missense_variant ENSG00000012048 ENST00000471181.6
chr17 43092418 T C ENST00000471181.6 missense_variant ENSG00000012048 ENST00000471181.6
chr17 43092919 G A ENST00000471181.6 missense_variant ENSG00000012048 ENST00000471181.6
chr17 43093220 A G ENST00000471181.6 synonymous_variant ENSG00000012048 ENST00000471181.6
chr17 43093449 G A ENST00000471181.6 synonymous_variant ENSG00000012048 ENST00000471181.6
chr17 43093454 C T ENST00000471181.6 missense_variant ENSG00000012048 ENST00000471181.6
chr17 43097077 A G ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43097346 TA T ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43099629 T A ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43104083 AAAG A ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43121331 T C ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43121362 G C ENST00000471181.6 intron_variant ENSG00000012048 ENST00000471181.6
chr17 43127281 A G ENST00000471181.6 upstream_gene_variant ENSG00000012048 ENST00000471181.6
chr17 43129737 G A ENST00000471181.6 upstream_gene_variant ENSG00000012048 ENST00000471181.6
chr17 43131360 C T ENST00000587322.1 downstream_gene_variant ENSG00000198496 ENST00000587322.1
chr17 43131380 AAAT A ENST00000587322.1 downstream_gene_variant ENSG00000198496 ENST00000587322.1
chr17 43135863 A G ENST00000587322.1 downstream_gene_variant ENSG00000198496 ENST00000587322.1
chr17 43138596 G T ENST00000356906.7 intron_variant&non_coding_transcript_variant ENSG00000198496 ENST00000356906.7
chr17 43138657 G C ENST00000356906.7 splice_region_variant&non_coding_transcript_exon_variant ENSG00000198496 ENST00000356906.7
chr17 43140410 C G ENST00000464237.2 upstream_gene_variant ENSG00000267681 ENST00000464237.2
chr17 43140722 G A ENST00000464237.2 upstream_gene_variant ENSG00000267681 ENST00000464237.2
chr17 43142914 TTG T ENST00000464237.2 upstream_gene_variant ENSG00000267681 ENST00000464237.2
chr17 43142940 G A ENST00000464237.2 upstream_gene_variant ENSG00000267681 ENST00000464237.2
chr17 43142964 GTGTATATATA G ENST00000464237.2 upstream_gene_variant ENSG00000267681 ENST00000464237.2
chr17 43145635 A C ENST00000464237.2 downstream_gene_variant ENSG00000267681 ENST00000464237.2
chr17 43145975 G T ENST00000464237.2 downstream_gene_variant ENSG00000267681 ENST00000464237.2
chr17 43146482 G A ENST00000464237.2 downstream_gene_variant ENSG00000267681 ENST00000464237.2
chr17 43147572 C T ENST00000464237.2 downstream_gene_variant ENSG00000267681 ENST00000464237.2
chr17 43147590 A G ENST00000464237.2 downstream_gene_variant ENSG00000267681 ENST00000464237.2
chr17 43147814 C CCT ENST00000464237.2 downstream_gene_variant ENSG00000267681 ENST00000464237.2
chr17 43147911 G C ENST00000464237.2 downstream_gene_variant ENSG00000267681 ENST00000464237.2
chr17 43152446 T C ENST00000467245.5 intron_variant&non_coding_transcript_variant ENSG00000198496 ENST00000467245.5
chr17 43169893 C T ENST00000341165.10 upstream_gene_variant ENSG00000188554 ENST00000341165.10
9 changes: 9 additions & 0 deletions tests/test_data/vep_annotation_reporter/preferred_transcripts.list.tsv
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Original file line number Diff line number Diff line change
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transcript_id
ENST00000587322.1
ENST00000471181.6
ENST00000467245.5
ENST00000464237.2
ENST00000413465.6
ENST00000356906.7
ENST00000341165.10
ENST00000269305.8
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