SNPSIFT(1) User Commands SNPSIFT(1)

snpSift - tool to annotate and manipulate genome variants

snpSift [command] [options] [files]

Create an allele matrix output.
Annotate 'ID' from a database (e.g. dbSnp). Assumes entries are sorted.
Compare how many variants are in 'case' and in 'control' groups; calculate p-values.
Case control summary. Case and control summaries by region, allele frequency and variant's functional effect.
Concordance metrics between two VCF files.
Create an covariance matrix output (allele matrix as input).
Annotate with multiple entries from dbNSFP.
Extract fields from VCF file into tab separated format.
Filter using arbitrary expressions
Annotate using MSigDb gene sets (MSigDb includes: GO, KEGG, Reactome, BioCarta, etc.)
Add Genotype to INFO fields and remove genotype fields when possible.
Filter genotype using arbitrary expressions.
Annotate using GWAS catalog
Calculate Hardy-Weimberg parameters and perform a godness of fit test.
Intersect intervals (genomic regions).
Keep variants that intersect with intervals. intIdx
join
op
phastCons
private
rmRefGen
rmInfo
sort
split
tstv
varType
vcfCheck
vcf2tped

Specify config file. Default: ~/.snpEff/snpEff.config
Debug mode.
Database file name (for commands that require databases).
Override a config file option
Download a SnpEff database, if not available locally. Default: true
Genome version (for commands that require databases).
Do not download a SnpEff database, if not available locally.
Do not report usage statistics to server
Show this help and exit
Verbose mode
Show version number and exit

https://pcingola.github.io/SnpEff/se_introduction/

snpeff(1)

This manual page was written by Pierre Gruet <pgt@debian.org> from the Debian project, but may be used by others. Please report possibly missing or misleading information.

February 2022 snpSift