Thomas
ddc5410ec4
0 in vcf
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| jq_filters | il y a 1 an | |
| src | il y a 1 an | |
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| Cargo.lock | il y a 1 an | |
| Cargo.toml | il y a 1 an | |
| README.md | il y a 1 an |
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]'