Skip to content

Commit

Permalink
README updates
Browse files Browse the repository at this point in the history
  • Loading branch information
sigven committed Dec 29, 2023
1 parent 3eb0c16 commit f09a043
Showing 1 changed file with 5 additions and 5 deletions.
10 changes: 5 additions & 5 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -34,8 +34,8 @@ The generic variant annotator (*gvanno*) is a software package intended for simp

### Annotation resources (v1.7.0)

- [VEP](http://www.ensembl.org/info/docs/tools/vep/index.html) - Variant Effect Predictor v109 (GENCODE v44/v19 as the gene reference dataset)
- [dBNSFP](https://sites.google.com/site/jpopgen/dbNSFP) - Database of non-synonymous functional predictions (v4.5, October 2023)
- [VEP](http://www.ensembl.org/info/docs/tools/vep/index.html) - Variant Effect Predictor v110 (GENCODE v44/v19 as the gene reference dataset)
- [dBNSFP](https://sites.google.com/site/jpopgen/dbNSFP) - Database of non-synonymous functional predictions (v4.5, November 2023)
- [gnomAD](http://gnomad.broadinstitute.org/) - Germline variant frequencies exome-wide (release 2.1, October 2018) - from VEP
- [dbSNP](http://www.ncbi.nlm.nih.gov/SNP/) - Database of short genetic variants (build 154) - from VEP
- [ClinVar](http://www.ncbi.nlm.nih.gov/clinvar/) - Database of variants related to human health/disease phenotypes (December 2023)
Expand Down Expand Up @@ -97,7 +97,7 @@ The generic variant annotator (*gvanno*) is a software package intended for simp
* `docker pull sigven/gvanno:1.7.0` (gvanno annotation engine)

* Singularity
* Download the [gvanno SIF image (v1.7.0)_](https://insilico.hpc.uio.no/pcgr/gvanno/gvanno_1.7.0.sif) (approx 1.3Gb) and use this as the argument for `--sif_file` in the `gvanno.py` run script.
* Download the [gvanno SIF image (v1.7.0)](https://insilico.hpc.uio.no/pcgr/gvanno/gvanno_1.7.0.sif) (approx 1.2Gb) and use this as the argument for `--sif_file` in the `gvanno.py` run script.



Expand Down Expand Up @@ -200,8 +200,8 @@ python ~/gvanno-1.7.0/gvanno.py

This command will run the Docker-based *gvanno* workflow and produce the following output files in the *examples* folder:

1. **example_gvanno_grch37.pass.vcf.gz (.tbi)** - Bgzipped VCF file with rich set of functional/clinical annotations
2. **example_gvanno_grch37.pass.tsv.gz** - Compressed TSV file with rich set of functional/clinical annotations
1. **example_gvanno_grch37.pass.vcf.gz (.tbi)** - Bgzipped VCF file with rich set of functional/clinical variant and gene annotations
2. **example_gvanno_grch37.pass.tsv.gz** - Compressed TSV file with rich set of functional/clinical variant and gene annotations

Similar files are produced for all variants, not only variants with a *PASS* designation in the VCF FILTER column.

Expand Down

0 comments on commit f09a043

Please sign in to comment.