snpSift1
Tool to annotate and manipulate genome variants
Usage
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