Screen for mutations of interest in SARS-CoV-2 sequencing results
python setup.py install
This script will recursively search a directory structure for variants files (ivar variant.tsv files, or nanopore .pass.vcf.gz files) and print out any samples that match a variant in a defined "watchlist" VCF file. For example this command will search for samples that contain one of the mutations defining the B.1.1.7 variant:
ncov-watch --mutation_set uk_variant --directory data 2>/dev/null
Alternatively you can pass the variant files on stdin:
find data/ -name "*.variants.tsv" | ncov-watch -m uk_variant 2>/dev/stderr
(note 2>/dev/stderr is to silence pysam warnings when parsing VCF files).
The built-in watchlists can be seen here. You can also use your own watchlist by providing -m with the path to a local VCF.