Tools for filtering VCF files
16 Jan 2013Tools for filtering VCF files:
- vcfutils.pl varFilter– A pretty basic script included with samtools to do VCF filtering. Not really useful enough for real work.
- vcftools– A fairly complete set of perl scripts for doing common VCF filtering tasks, particularly with vcf-annotate module. Couldn’t find a way of doing per-sample filtering however.
- PyVCF– comes with a useful script vcf_filter.py which permits per-sample filtering. Provides API to add your own specialised filters written in Python.
- GATK– complex does-everything solution with extensive variant filtering options
- SnpSift– permits SNP filtering with expressions, seems fairly basic, able to also filter based on output of partner software SnpEff (http://snpeff.sourceforge.net/SnpSift.html) (HT:@daweonline)
- VarScan– not technically a VCF filter as takes samtools mpileup as input, but has some useful SNP based filters with sensible defaults.
- vcflib - includes vcffilter tool which I haven’t tried