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.