pandora_lib_promethion/README.md

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(contig("chrM") and n_in_constit <= 1) | format]'