BioInformatics Tools
Installation
python3 -m pip install bioinfo-toolset
Usage
Example
bit vep -l ENST00000257430.9:c.3927_3931del
Result for ENST00000257430.9:c.3927_3931del
GRCh38: ENST00000257430.9:c.3927_3931del -> 5:112839521-112839525 (AAAGA > -)
GRCh37: ENST00000257430.9:c.3927_3931del -> 5:112175218-112175222 (AAAGA > -)
assembly_name : GRCh38
id : ENST00000257430.9:c.3927_3931del
seq_region_name : 5
start : 112839521
end : 112839525
allele_string : AAAGA/-
strand : 1
most_severe_consequence : frameshift_variant
Colocated variants (1):
id : COSV57321812
seq_region_name : 5
start : 112839521
end : 112839525
allele_string : COSMIC_MUTATION
strand : 1
somatic : 1
---
Transcript consequences (8):
transcript_id : ENST00000257430
gene_symbol : APC
gene_id : ENSG00000134982
hgnc_id : HGNC:583
amino_acids : EKI/DX
consequence_terms : [' frameshift_variant' ]
protein_position : 1309-1311
transcript_name : EKI1309-1311DX
---
transcript_id : ENST00000502371
gene_symbol : APC
gene_id : ENSG00000134982
hgnc_id : HGNC:583
consequence_terms : [' 3_prime_UTR_variant' , ' NMD_transcript_variant' ]
protein_position : N/A
transcript_name : N/A
---
transcript_id : ENST00000504915
gene_symbol : APC
gene_id : ENSG00000134982
hgnc_id : HGNC:583
consequence_terms : [' downstream_gene_variant' ]
protein_position : N/A
transcript_name : N/A
---
transcript_id : ENST00000507379
gene_symbol : APC
gene_id : ENSG00000134982
hgnc_id : HGNC:583
consequence_terms : [' downstream_gene_variant' ]
protein_position : N/A
transcript_name : N/A
---
transcript_id : ENST00000508376
gene_symbol : APC
gene_id : ENSG00000134982
hgnc_id : HGNC:583
amino_acids : EKI/DX
consequence_terms : [' frameshift_variant' ]
protein_position : 1309-1311
transcript_name : EKI1309-1311DX
---
transcript_id : ENST00000508624
gene_symbol : APC
gene_id : ENSG00000134982
hgnc_id : HGNC:583
consequence_terms : [' 3_prime_UTR_variant' , ' NMD_transcript_variant' ]
protein_position : N/A
transcript_name : N/A
---
transcript_id : ENST00000512211
gene_symbol : APC
gene_id : ENSG00000134982
hgnc_id : HGNC:583
consequence_terms : [' downstream_gene_variant' ]
protein_position : N/A
transcript_name : N/A
---
transcript_id : ENST00000520401
gene_id : ENSG00000258864
consequence_terms : [' intron_variant' , ' NMD_transcript_variant' ]
protein_position : N/A
transcript_name : N/A
---