## 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_variants"; [.data[] | select(contig("chrM") and n_in_constit <= 1) | format]'
```

### Using jq and find to look for chrM norm coverage
```
find /data/longreads_basic_pipe/ -name "*_diag_hs1_info.json" -type f -exec sh -c 'basename $(dirname $(dirname "{}")) | tr -d "\n"' \; -printf "\t" -exec jq -L ./jq_filters -r 'include "jq_bam"; contig_coverage("chrM")' {} \;
```

### Reading log files
```
zcat /data/longreads_basic_pipe/ID/log/deepsomatic/deepvariant_e7ed1.log.gz | jq -r '.log'

```