Commit 92dd2ec7 authored by Pradat Yoann's avatar Pradat Yoann

add info in README

parent f2161e4c
......@@ -12,7 +12,6 @@ The tool is divided in 3 steps
VEP annotates variants with information from multiple external databases and can be configure for to answer a lot of specific needs. For more details,
see [VEP's options page](https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html). VEP does not however extract information like number of reads or somatic status from the VCF file. vcf2maf is supposed to perform these tasks but failed to do on quite a lot of example VCF and does not always extract all the relevant information. For this reason, manual parsing was implemented in Python and was tested on TCGA VCF files from the legacy archive portal (see examples) and other VCFs. See the table for exhaustive details.
### 1.2. vcf2maf
vcf2maf also runs VEP internally but performs extra work to build some annotation fields including the following
......@@ -32,6 +31,8 @@ vcf2maf also runs VEP internally but performs extra work to build some annotatio
- *HGVS_Short*
- *all_effects*
that are not available from VEP's output.
### 1.3. VEP
Run the VEP annotator on the VCF file from a specific set of options. The options can be changed in the code if required.
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment