Adding expression data to your VCF¶
pVACseq is able to parse coverage and expression information directly from the VCF. The expected annotation format is outlined below.
Type |
VCF Sample |
Format Fields |
|---|---|---|
Transcript Expression |
single-sample VCF or |
|
Gene Expression |
single-sample VCF or |
|
Transcript Expression
If the VCF is a single-sample VCF, pVACseq assumes that this sample is the
tumor sample. If the VCF is a multi-sample VCF, pVACseq will look for the
sample using the sample_name parameter and treat that sample as the tumor
sample.
For this tumor sample the transcript expression is determined from the TX
format field. The TX format field is a comma-separated list of
per-transcript expression values, where each individual transcript expression
is listed as expression_id|expression_value, e.g.
ENST00000215794|2.35912,ENST00000215795|0.2. The expression_id needs
to match the Feature field of the VEP CSQ annotation. In other words,
your expression abundance estimation should have been performed with the same transcript
annotation version that you used to annotate your variants with VEP (e.g. Ensembl v95).
Gene Expression
If the VCF is a single-sample VCF, pVACseq assumes that this sample is the
tumor sample. If the VCF is a multi-sample VCF, pVACseq will look for the
sample using the sample_name parameter and treat that sample as the tumor
sample.
For this tumor sample the gene expression is determined from the GX
format field. The GX format field is a comma-separated list of
per-gene expression values, where each individual gene expression
is listed as gene_id|expression_value, e.g.
ENSG00000184979|2.35912. The gene_id needs to match the Gene field
of the VEP CSQ annotation.
Using the vcf-expression-annotator to add expression information to your VCF¶
The vcf-expression-annotator will add expression information to your VCF.
It will accept expression data from various tools. Currently it supports
Cufflinks, Kallisto, StringTie, as well as a custom option for any
tab-delimited file.
Installing the vcf-expression-annotator¶
The vcf-expression-annotator is part of the vatools package (vatools.org).
You can install this package by running:
pip install vatools
Running the vcf-expression-annotator¶
You can now use the output file from your expression caller to add expression information to your VCF:
vcf-expression-annotator input_vcf expression_file kallisto|stringtie|cufflinks|custom gene|transcript
The data type gene or transcript identifies whether you are annotating
transcript or gene expression data. Transcript expression annotations will be
written to the TX format field while gene expression annotations will be
written to the GX format field. Please see the VAtools documentation
for more information.