exoclasma-note

Name	exoclasma-note JSON
Version	0.9.0 JSON
	download
home_page
Summary	Exo-C Data Quality Check, Mapping, and Variant Calling, part of ExoClasma Suite
upload_time	2023-01-11 10:36:09
maintainer
docs_url	None
author
requires_python	>=3.8
license
keywords	annotation bioinformatics variant
VCS
bugtrack_url
requirements	No requirements were recorded.
Travis-CI	No Travis.
coveralls test coverage	No coveralls.

            # exoclasma-note

Annotation of genomic variants.

## Dependencies

Perl:

```bash
sudo apt install perl
```

Annovar:

```bash
GENOME="hg19" # hg38 if you prefer
curl --output annovar.latest.tar.gz www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.latest.tar.gz
tar -xzf annovar.latest.tar.gz
cd annovar
for database in refGene knownGene ensGene dbnsfp35c dbscsnv11 intervar_20180118 gnomad211_genome gene4denovo201907 kaviar_20150923 hrcr1 abraom 1000g2015aug gme esp6500siv2_all avsnp150 clinvar_20200316 regsnpintron revel gwava;
do {
	perl annotate_variation.pl -downdb -buildver ${GENOME} -webfrom annovar ${database} humandb/
} done
cd ..
rm annovar.latest.tar.gz
```

## Install

```bash
sudo python3 -m pip install exoclasma-note
```

## Usage

```bash
exoclasma-note -u ${unit_json} -a ${annovar_folder} -g ${genome} [--nofilter]
```

* `unit_json`: Unit JSON file which was created by exoclasma-pipe
* `annovar_folder`: Path to ANNOVAR folder where perl scripts are located
* `genome`: Genome assembly which use ANNOVAR (i.e., hg19, hg38, etc.)

            

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