README.md 977 B
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")' {} \;