Introduction - SnpEff & SnpSift
Author: Pablo Cingolani
Description: SnpEff and SnpSift

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# SnpSift

SnpSift is a toolbox that allows you to filter and manipulate annotated files.

Once your genomic variants have been annotated, you need to filter them out in order to find the "interesting / relevant variants". Given the large data files, this is not a trivial task (e.g. you cannot load all the variants into XLS spreadsheet). SnpSift helps to perform this VCF file manipulation and filtering required at this stage in data processing pipelines.

### Download and install

SnpSift is part of SnpEff main distribution, so please click on here and follow the instructions on how to download and install SnpEff.

### SnpSift utilities

SnpSift is a collection of tools to manipulate VCF (variant call format) files.

Some examples of what you can do:

Operation | Meaning
--- | ---
Filter | You can filter using arbitrary expressions, for instance `"(QUAL > 30) | (exists INDEL) | ( countHet() < 2 )"`. The actual expressions can be quite complex, so it allows for a lot of flexibility.
Annotate | You can add 'ID' and INFO fields from another "VCF database" (e.g. typically dbSnp database in VCF format).
CaseControl | You can compare how many variants are in 'case' and in 'control' groups. Also calculates p-values (Fisher exact test).
Intervals | Filter variants that intersect with intervals.
Intervals (intidx) | Filter variants that intersect with intervals. Index the VCF file using memory mapped I/O to speed up the search. This is intended for huge VCF files and a small number of intervals to retrieve.
Join | Join by generic genomic regions (intersecting or closest).
RmRefGen | Remove reference genotype (i.e. replace '0/0' genotypes by '.')
TsTv | Calculate transition to transversion ratio.
Extract fields | Extract fields from a VCF file to a TXT (tab separated) format.
Variant type | Adds SNP/MNP/INS/DEL to info field. It also adds "HOM/HET" if there is only one sample.
GWAS Catalog | Annotate using GWAS Catalog.
DbNSFP | Annotate using dbNSFP: The dbNSFP is an integrated database of functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.)
SplitChr | Split a VCF file by chromosome

### Citing SnpSift

In order to cite SnpSift, please use the following example.

### Source code

The project is hosted at GitHub.