bystro-snp

TL;DR

A really fast, simple SNP pre-processor and annotator. Millions of variants per minute.

go get github.com/akotlar/bystro-snp && go install $_;

pigz -d -c in.snp.gz | bystro-snp --minGq .95 | pigz -c - > output 2> log.txt

Description

Performs several important functions:

1. Splits multiallelics
2. Performs QC on variants: checks whether allele is ACTG, +ACTG, or -Int
3. Filters samples based on genotype quality
4. Calculates whether site is transition, transversion, or neither
5. Processes all available samples
   • calculates homozygosity, heterozygosity, missingness
   • labels samples as homozygous, heterozygous, or missing

Publication

bystro-snp is used to pre-proces SNP files for Bystro (github)

If you use bystro-snp please cite https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1387-3

Performance

Millions of variants/rows per minute. Performance is dependent on the # of samples.

Installation

go get github.com/akotlar/bystro-snp && go install $_;

Use

Via pipe:

pigz -d -c in.snp.gz | bystro-snp --minGq .95 | pigz -c - > out.gz

Via inPath argument:

bystro-snp --inPath in.snp --minGq .95 " > out

Output

chrom <String>   pos <Int>   type <String[SNP|DEL|INS|MULTIALLELIC]>    ref <String>    alt <String>    trTv <Int[0|1|2]>     heterozygotes <String>     heterozygosity <Float64>    homozygotes <String>     homozygosity <Float64>     missingGenos <String>    missingness <Float64>    sampleMaf <Float64>

Optional arguments

--minGq <Float>

Minimum genotype quality to keep (0 - 1)

--inPath /path/to/uncompressedFile.snp

An input file path, to an uncompressed VCF file. Defaults to stdin

--errPath /path/to/log.txt

Where to store log messages. Defaults to STDERR

--emptyField "!"

Which value to assign to missing data. Defaults to !

--fieldDelimiter ";"

Which delimiter to use when joining multiple values. Defaults to ;