Mercurial > repos > jjohnson > snpsift
changeset 1:796388c291d3
Update for snpeff version 4.0
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 20 Oct 2014 08:43:00 -0500 |
| parents | 1ae5526db990 |
| children | 49b5bd3dc316 |
| files | snpEff_macros.xml snpSift_annotate.xml snpSift_caseControl.xml snpSift_filter.xml snpSift_int.xml tool_dependencies.xml |
| diffstat | 6 files changed, 37 insertions(+), 15 deletions(-) [+] |
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--- a/snpEff_macros.xml Thu Jun 26 09:22:13 2014 -0400 +++ b/snpEff_macros.xml Mon Oct 20 08:43:00 2014 -0500 @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="3.6">snpEff</requirement> + <requirement type="package" version="4.0">snpEff</requirement> </requirements> </xml> <xml name="stdio">
--- a/snpSift_annotate.xml Thu Jun 26 09:22:13 2014 -0400 +++ b/snpSift_annotate.xml Mon Oct 20 08:43:00 2014 -0500 @@ -1,4 +1,4 @@ -<tool id="snpSift_annotate" name="SnpSift Annotate" version="3.6"> +<tool id="snpSift_annotate" name="SnpSift Annotate" version="4.0.0"> <description>SNPs from dbSnp</description> <!-- You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
--- a/snpSift_caseControl.xml Thu Jun 26 09:22:13 2014 -0400 +++ b/snpSift_caseControl.xml Mon Oct 20 08:43:00 2014 -0500 @@ -1,4 +1,4 @@ -<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.6"> +<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="4.0.0"> <description>Count samples are in 'case' and 'control' groups.</description> <!-- You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
--- a/snpSift_filter.xml Thu Jun 26 09:22:13 2014 -0400 +++ b/snpSift_filter.xml Mon Oct 20 08:43:00 2014 -0500 @@ -1,4 +1,4 @@ -<tool id="snpSift_filter" name="SnpSift Filter" version="3.6"> +<tool id="snpSift_filter" name="SnpSift Filter" version="4.0.0"> <options sanitize="False" /> <description>Filter variants using arbitrary expressions</description> <expand macro="requirements" /> @@ -50,7 +50,7 @@ </inputs> <configfiles> <configfile name="exprFile"> - $expr +$expr#slurp </configfile> </configfiles> @@ -119,13 +119,36 @@ 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*: :: @@ -151,12 +174,11 @@ (isHom( GEN[0] ) & isVariant( GEN[0] ) & isRef( GEN[1] )) - - *I want to filter lines with an EFF of FRAME_SHIFT*: +**For information regarding HGVS and Sequence Ontology terms versus classic names**: - :: - - ( EFF[*].EFFECT = 'FRAME_SHIFT' ) - + - 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
--- a/snpSift_int.xml Thu Jun 26 09:22:13 2014 -0400 +++ b/snpSift_int.xml Mon Oct 20 08:43:00 2014 -0500 @@ -1,4 +1,4 @@ -<tool id="snpSift_int" name="SnpSift Intervals" version="3.6"> +<tool id="snpSift_int" name="SnpSift Intervals" version="4.0.0"> <description>Filter variants using intervals</description> <!-- You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
--- a/tool_dependencies.xml Thu Jun 26 09:22:13 2014 -0400 +++ b/tool_dependencies.xml Mon Oct 20 08:43:00 2014 -0500 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> - <package name="snpEff" version="3.6"> - <repository name="package_snpeff_3_6" owner="jjohnson" changeset_revision="849895b37940" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + <package name="snpEff" version="4.0"> + <repository name="package_snpeff_4_0" owner="jjohnson" changeset_revision="4ac635fc1781" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> </package> </tool_dependency>