comparison snpSift_filter.xml @ 1:796388c291d3

Update for snpeff version 4.0

0:1ae5526db990

<tool id="snpSift_filter" name="SnpSift Filter" version="3.6">
    <options sanitize="False" />
    <description>Filter variants using arbitrary expressions</description>
    <expand macro="requirements" />
    <macros>
        <import>snpEff_macros.xml</import>

            </when>
        </conditional>
    </inputs>
    <configfiles>
        <configfile name="exprFile">
        $expr
        </configfile> 
    </configfiles>

    <outputs>
        <data format="vcf" name="output" />

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 )

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


  - *I want to filter lines with an EFF of FRAME_SHIFT*:

    ::
  
    ( EFF[*].EFFECT = 'FRAME_SHIFT' )
  

@EXTERNAL_DOCUMENTATION@
	http://snpeff.sourceforge.net/SnpSift.html#filter

@CITATION_SECTION@

1:796388c291d3

<tool id="snpSift_filter" name="SnpSift Filter" version="4.0.0">
    <options sanitize="False" />
    <description>Filter variants using arbitrary expressions</description>
    <expand macro="requirements" />
    <macros>
        <import>snpEff_macros.xml</import>

            </when>
        </conditional>
    </inputs>
    <configfiles>
        <configfile name="exprFile">
$expr#slurp
        </configfile> 
    </configfiles>

    <outputs>
        <data format="vcf" name="output" />

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 just the variants from the second million bases of chr1*:

    ::

    ( CHROM = 'chr1' ) & ( POS > 1000000 )  & ( POS < 2000000 )

  - *Filter value is either 'PASS' or it is missing*:

    ::

    (FILTER = 'PASS') | ( na FILTER )  

  - *I want to filter lines with an EFF of 'frameshift_variant' ( for vcf files using Sequence Ontology terms )*:

    ::
  
    ( EFF[*].EFFECT = 'frameshift_variant' )

  - *I want to filter lines with an EFF of 'FRAME_SHIFT' ( for vcf files using Classic Effect names )*:

    ::
  
    ( EFF[*].EFFECT = 'FRAME_SHIFT' )

  - *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 )

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


**For information regarding HGVS and Sequence Ontology terms versus classic names**:

  - http://snpeff.sourceforge.net/SnpEff_manual.html#cmdline for the options: -classic, -hgvs, and -sequenceOntology
  - http://snpeff.sourceforge.net/SnpEff_manual.html#input for the table containing the classic name and sequence onology term for each effect


@EXTERNAL_DOCUMENTATION@
	http://snpeff.sourceforge.net/SnpSift.html#filter

@CITATION_SECTION@