somAgg code book functional annotation queries¶
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We can use split-vep to query and parse the functional annotation from VEP.
bcftools version
Please use bcftools version 1.16 via: module load bcftools/1.16
Snippets
Within each snippet shown below, most lines end with the '\' character. This is not part of the command but a shorthand notation meaning "keep reading the next line as part of a single command." We do this to split each snippet over multiple lines so it is easier to read.
The queries below work with the functional annotation data files present in:
/gel_data_resources/main_programme/aggregation/aggregated_somatic_strelka/somAgg/v0.2/functional_annotation/VEP
View CellBase annotations¶
You can view all of the available CellBase annotations using the command below - all annotations can be extracted and/or filtered for. Note that, split-vep has been designed to work with VEP and VEP-like annotation. The Cellbase annotation provided in somAgg is VEP-like. This requires the annotation field to be given explicitly to split-vep, which is done by using the flag -a CT.
Output:
...
0 GeneName
1 TranscriptID
2 CDSchange
3 ProteinChange
4 Consequence
5 siftDescription
6 siftScore
7 polyphenDescription
8 polyphenScore
...
Extract variants for a gene of interest¶
Question: I want to extract all variants in the gene IKZF1 and view some basic annotation.
Script: Use bcftools split-vep. Use the flag -a CT to tell split-vep what the annotation field is called. This example will output variants annotated against all transcripts for the gene of interest - IKZF1 - using the -i flag. There will be one annotation per line (for each transcript - using the -d flag). The -f option formats the output with the attributes included. The > character writes the output to a tab-delimited file.
Output: The output is a tab-delimited file in long-format - where each annotation is on a separate line across all variants. The columns are in the same order as stated in the -f command above.
...
chr7 50299131 G A IKZF1 ENST00000484847 upstream_variant .
chr7 50299139 A AGT IKZF1 ENST00000484847 upstream_gene_variant .
chr7 50299147 C T IKZF1 ENST00000484847 upstream_variant .
chr7 50299148 G A IKZF1 ENST00000484847 upstream_variant .
...
* data have been randomised and subset
Extract variants for a gene of interest with a damaging prediction¶
Question: I want to view the variants that that are missense or worse in the gene IKZF1.
Script: Use bcftools split-vep. This example will output variants annotated against all transcripts for the gene of interest (IKZF1) that are missense or worse (-s and -S flag). Use the flag -a CT to tell split-vep what the annotation field is called. There will be one annotation per line (for each transcript - using the -d flag). The -f option formats the output with the attributes included. The > character writes the output to a tab-delimited file.
Output: The output is a tab-delimited file in long-format - where each annotation is on a separate line across all variants. The columns are in the same order as stated in the -f command above.
...
chr7 50327647 G T IKZF1 ENST00000413698 missense_variant p.(SER17ILE)
chr7 50327647 GC G IKZF1 ENST00000413698 frameshift_variant p.(SER17SER)
chr7 50327653 C T IKZF1 ENST00000413698 missense_variant p.(PRO19LEU)
chr7 50327661 G C IKZF1 ENST00000413698 missense_variant p.(ASP22HIS)
chr7 50327661 G A IKZF1 ENST00000413698 missense_variant p.(ASP22ASN)
...
* data have been randomised and subset
When using bcftools 1.11.x specifying severity constraints via the -s flag, as above, is redudant. However, you may refer to the example to provide your own severity scale if needed. The one above can be found at:
/gel_data_resources/main_programme/aggregation/aggregated_somatic_strelka/somAgg/v0.2/additional_data/vep_severity_scale/VEP_severity_scale_2020.txt
Extract variants for a gene of interest – Genomics England Interpretation pipeline¶
Question: I want to extract per sample variants as presented in the analysis_csv (LabKey table cancer_analysis) in the gene IKZF1.
Script: Use bcftools split-vep. This example will output variants annotated against all transcripts for the gene of interest (IKZF1) that are missense or worse (-s and -S flag). Use the flag -a CT to tell split-vep what the annotation field is called. There will be one annotation per line (for each transcript - using the -d flag). The -f option formats the output with the attributes included. The > character writes the output to a tab-delimited file.
Output: The output is a tab-delimited file in long-format - where each annotation is on a separate line across all variants. The columns are in the same order as stated in the -f command above.
...
chr7 50327647 G T IKZF1 ENST00000413698 missense_variant p.(SER17ILE)
chr7 50327647 GC G IKZF1 ENST00000413698 frameshift_variant p.(SER17SER)
chr7 50327653 C T IKZF1 ENST00000413698 missense_variant p.(PRO19LEU)
chr7 50327661 G C IKZF1 ENST00000413698 missense_variant p.(ASP22HIS)
chr7 50327661 G A IKZF1 ENST00000413698 missense_variant p.(ASP22ASN)
...
* data have been randomised and subset
The list of transcripts used by the Cancer Programme Genomics England Interpretation pipeline can be found here:
/gel_data_resources/main_programme/aggregation/aggregated_somatic_strelka/somAgg/v0.2/additional_data/LIST_OF_CANONICAL_TRANSCRIPTS.v1.11.tsv
Alternatively, the MANE project is also available on our HPC, at:
/public_data_resources/ensembl_cds/MANE/v0.95/