## Utilities / Filter and analyse variants

### Description

Filters and analyses variants in VCF files.

### Parameters

- Keep only indels (yes, no) [no]
- Remove indels (yes, no) [no]
- Filter by allele number (yes, no) [no]
- Minimum number of alleles (Integer) [0]
- Maximum number of alleles (Integer) [0]
- Report per-site frequency information (yes, no) [no]
- Report p-value (yes, no) [no]
- Report LD statistics (yes, no) [no]
- Report SNP density (Integer) [0]
- List removed files (yes, no) [no]

### Details

Filters VCF files by various criteria and calculates simple statistics.

### Output

Output is a VCF file. You can view VCF files in Chipster as text (which includes the header) or spreadsheet (which can be sorted). The location column in the spreadsheet can be used in Chipster genome browser to navigate quickly through a list of variants.

### References

This tool is based on the VCFtools package. Please cite the article The Variant Call Format and VCFtools by Danecek P., Auton A., Abecasis G, Albers C. A., Banks E., DePristo M. A., Handsaker R., Lunter G., Gabor Marth G., Sherry S. T., McVean G., Durbin R. and 1000 Genomes Project Analysis Group (2011) Bioinformatics, 27, 2156-8. [PMID: 21653522]