Filter variants with VCFtools

Description

Filters variants in VCF files.

Parameters

• Keep only indels (yes, no) [no]
• Remove indels (yes, no) [no]
• Minimum number of alleles (Integer) [0]
• Maximum number of alleles (Integer) [0]
• Minimum quality (Decimal) [0]
• Filter by flags (yes, no) [no]
• INFO fields to keep (none, concise, all) [concise]
• List removed sites (yes, no) [no]

Details

Filters VCF files by various criteria.

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.

Please note the INFO values may be invalidated by the filtering, e.g. the total depth may need to be recalculated if individuals are removed. You have the option to discard all INFO values, keep all or keep a concise set for ease of reading (default option).

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]