HGVSparse

Simple utility to parse HGVS to VCF (and optionally annotate them with local installation of [Ensembl-vep](https://github.com/Ensembl/ensembl-vep))

Usage example

For a quick example run the provided example.sh. This tool requires to have a fasta reference file (chrX provided) and an annotated transcript file The example focuses on MECP2 gene, here the GTF transcript file example, required to infer the mutation type:

0 NC_000023.11 X - 1 156040895 1 156040895 10 67092175,67096251,67103237,67111576,67113613,67115351,67125751,67127165,67131141,67134929, 6  7093604,67096321,67103382,67111644,67113756,67115464,67125909,67127257,67131227,67134971, 0 C1orf141 none none -1,-1,-1,-1,-1,-1,-1,-1,-1,-1,

The example also requires to specify region names to keep for parsing. In this case, we chose to process HGVS entries from NC_000023.11:g.,NM_004992.3:c. [-r line in example.sh ]

## example.sh ##
# 1st: unzip the fasta file
gzip -d example/chrX.fa.gz
# 2nd: make the output directory
mkdir -p example/results
# 3rd: run the conversion tool
sh HGVS_to_VEP.sh \
  -i example/variants_in.txt \
  -o example/results \
  -p test \
  -g example/chrX.fa \
  -t example/chrx.txt \
  -r NC_000023.11:g.,NM_004992.3:c.

Run with VEP local annotaion

This requires a local installation of Ensembl-vep with the appropriate cache and fasta references. It also requires to have dbNSFP and dbscSNV plugins installed. To add the VEP annotation, add a -v flag to the execution line of HGVS_to_VEP.sh call