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SnpSift Filter (version 3.3)

VCF input:

Expression:

Inverse. Show lines that do not match filter expression:

Use 'PASS' field instead of filtering out VCF entries:

ID for this filter (##FILTER tag in header and FILTER VCF field).:

Add a string to FILTER VCF field if 'expression' is true.:

Remove a string from FILTER VCF field if 'expression' is true (and 'str' is in the field).:

SnpSift filter

You can filter ia vcf file 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.

Some examples:

I want to filter out samples with quality less than 30:

( QUAL > 30 )

...but we also want InDels that have quality 20 or more:

(( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )

...or any homozygous variant present in more than 3 samples:

(countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )

...or any heterozygous sample with coverage 25 or more:

((countHet() > 0) & (DP >= 25)) | (countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )

I want to keep samples where the genotype for the first sample is homozygous variant and the genotype for the second sample is reference:

isHom( GEN[0] ) & isVariant( GEN[0] ) & isRef( GEN[1] )

For complete details about this tool and expressions that can be used, please read the fine manual http://snpeff.sourceforge.net/SnpSift.html#filter

For details about this tool, please see the snpEff web site.