| SNPSIFT(1) | User Commands | SNPSIFT(1) |
NAME¶
snpSift - tool to annotate and manipulate genome variants
SYNOPSIS¶
snpSift [command] [options] [files]
AVAILABLE COMMANDS¶
- alleleMat
- Create an allele matrix output.
- annotate
- Annotate 'ID' from a database (e.g. dbSnp). Assumes entries are sorted.
- caseControl
- Compare how many variants are in 'case' and in 'control' groups; calculate p-values.
- ccs
- Case control summary. Case and control summaries by region, allele frequency and variant's functional effect.
- concordance
- Concordance metrics between two VCF files.
- covMat
- Create an covariance matrix output (allele matrix as input).
- dbnsfp
- Annotate with multiple entries from dbNSFP.
- extractFields
- Extract fields from VCF file into tab separated format.
- filter
- Filter using arbitrary expressions
- geneSets
- Annotate using MSigDb gene sets (MSigDb includes: GO, KEGG, Reactome, BioCarta, etc.)
- gt
- Add Genotype to INFO fields and remove genotype fields when possible.
- gtfilter
- Filter genotype using arbitrary expressions.
- gwasCat
- Annotate using GWAS catalog
- hwe
- Calculate Hardy-Weimberg parameters and perform a godness of fit test.
- intersect
- Intersect intervals (genomic regions).
- intervals
- Keep variants that intersect with intervals. intIdx
- Keep variants that intersect with intervals. Index-based method: Used for large VCF file and a few intervals to retrieve
- join
- Join files by genomic region.
- op
- Annotate using an operator.
- phastCons
- Annotate using conservation scores (phastCons).
- private
- Annotate if a variant is private to a family or group.
- rmRefGen
- Remove reference genotypes.
- rmInfo
- Remove INFO fields.
- sort
- Sort VCF file/s (if multiple input VCFs, merge and sort).
- split
- Split VCF by chromosome.
- tstv
- Calculate transition to transversion ratio.
- varType
- Annotate variant type (SNP,MNP,INS,DEL or MIXED).
- vcfCheck
- Check that VCF file is well formed.
- vcf2tped
- Convert VCF to TP
OPTIONS¶
Generic options¶
- -c , -config
- Specify config file. Default: ~/.snpEff/snpEff.config
- -d , -debug
- Debug mode.
- -db <file> , -database <file>
- Database file name (for commands that require databases).
- -configOption name=value
- Override a config file option
- -download
- Download a SnpEff database, if not available locally. Default: true
- -g <name> , -genome <name>
- Genome version (for commands that require databases).
- -nodownload
- Do not download a SnpEff database, if not available locally.
- -noLog
- Do not report usage statistics to server
- -h , -help
- Show this help and exit
- -v , -verbose
- Verbose mode
- -version
- Show version number and exit
SEE ALSO¶
https://pcingola.github.io/SnpEff/se_introduction/
snpeff(1)
AUTHOR¶
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 |