## Install

### Dependencies

For building required HTSlib:
```
sudo apt install cmake libclang-dev

```

* minimap2 
* (samtools)[https://www.htslib.org/download/]
* (dorado)[https://github.com/nanoporetech/dorado]
* (bcftools)[https://www.htslib.org/download/]
* (modkit)[https://github.com/nanoporetech/modkit]
* VEP: cf pandora_lib_variants for VEP install
* nanomonsv (cf dependencies at github, TODO: use racon)

## Usage

### Use jq for selecting variants:

* Somatic Variants of chrM (25) 
```
zcat /data/longreads_basic_pipe/*/diag/somatic_variants.json.gz | \
jq -L ./jq_filters -C 'include "jq_filters"; [.data[] | select(.position.contig == 25 and n_in_constit <= 1) | format]'
```