vcfilter

• asynchronous population scale variant filter. It reports stats on the top of the file and gives you the following for each file in the folder:

• sample1.alt-stats: stats on alt allele

• sample1.alt-unique-variants.txt: unique alt allele in that vcf to see after filtering which are the variant types present.

• sample1.filtereds: filtered file according to the variants and coverage or quality or zygosity

• sample1.ref-stats: stat on ref allele

• sample1.ref-unique-variants.txt: unique ref allele in that vcf to see after filtering which are the variant types present.

• Scientific Rust

_____   _   _   _
__   __   ___  |  ___| (_) | | | |_    ___   _ __
\ \ / /  / __| | |_    | | | | | __|  / _ \ | '__|
\ V /  | (__  |  _|   | | | | | |_  |  __/ | |
\_/    \___| |_|     |_| |_|  \__|  \___| |_|


asynchronous vcf filter for human genomics.
************************************************
Gaurav Sablok, IBCH, PAN, Poznan, Poland,
https://portal.ichb.pl/laboratory-of-genomics/.
Email: gsablok@ibch.poznan.pl
************************************************

Usage: vcfilter <COMMAND>

Commands:
default-vcf-filter           vcf filter according to quality, coverage and zygosity
quality-vcf-filter           vcf filter according to quality
coverage-vcf-filter          vcf filter according to coverage
zygosity-vcf-filter          vcf filter according to zygosity
variant-default-vcf-filter   vcf filter default quality40, coverage10 and zygosity multi
variant-quality-vcf-filter   vcf filter according to quality and variant
variant-coverage-vcf-filter  vcf filter according to coverage and variant
variant-zygosity-vcf-filter  vcf filter according to zygosity and variant
help                         Print this message or the help of the given subcommand(s)

Options:
-h, --help     Print help
-V, --version  Print version

./target/debug/vcfilter sample-files 47
./target/debug/vcfilter variant-coverage-vcf-filter sample-files 47 A

• To install windows version:

rustup component add llvm-tools
rustup target add x86_64-pc-windows-msvc
git clone https://github.com/IBCHgenomic/vcfilter.git
cd ensemblcov
cargo xwin build --target x86_64-pc-windows-msvc

Gaurav Sablok
Instytut Chemii Bioorganicznej
Polskiej Akademii Nauk
ul. Noskowskiego 12/14 | 61-704, Poznań
Poland