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changeset 33:642c7f54431a draft default tip

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Uploaded
author david-hoover
date Thu, 20 Sep 2012 13:23:44 -0400
parents 29507d31c174
children
files base_recalibrator.xml depth_of_coverage.xml indel_realigner.xml print_reads.xml realigner_target_creator.xml unified_genotyper.xml variant_annotator.xml variant_apply_recalibration.xml variant_combine.xml variant_eval.xml variant_filtration.xml variant_recalibrator.xml variant_select.xml variants_validate.xml
diffstat 14 files changed, 15 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- a/base_recalibrator.xml	Thu Sep 20 12:03:32 2012 -0400
+++ b/base_recalibrator.xml	Thu Sep 20 13:23:44 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_base_recalibrator" name="Base Recalibrator" version="0.0.3">
+<tool id="gatk2_base_recalibrator" name="Base Recalibrator" version="0.0.4">
   <description>on BAM files</description>
   <requirements>
       <requirement type="package" version="2.1">gatk</requirement>
--- a/depth_of_coverage.xml	Thu Sep 20 12:03:32 2012 -0400
+++ b/depth_of_coverage.xml	Thu Sep 20 13:23:44 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="0.0.3">
+<tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="0.0.4">
   <description>on BAM files</description>
   <requirements>
       <requirement type="package" version="2.1">gatk</requirement>
--- a/indel_realigner.xml	Thu Sep 20 12:03:32 2012 -0400
+++ b/indel_realigner.xml	Thu Sep 20 13:23:44 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_indel_realigner" name="Indel Realigner" version="0.0.3">
+<tool id="gatk2_indel_realigner" name="Indel Realigner" version="0.0.4">
   <description>- perform local realignment</description>
   <requirements>
       <requirement type="package" version="2.1">gatk</requirement>
--- a/print_reads.xml	Thu Sep 20 12:03:32 2012 -0400
+++ b/print_reads.xml	Thu Sep 20 13:23:44 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_print_reads" name="Print Reads" version="0.0.3">
+<tool id="gatk2_print_reads" name="Print Reads" version="0.0.4">
   <description>on BAM files</description>
   <requirements>
       <requirement type="package" version="2.1">gatk</requirement>
--- a/realigner_target_creator.xml	Thu Sep 20 12:03:32 2012 -0400
+++ b/realigner_target_creator.xml	Thu Sep 20 13:23:44 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_realigner_target_creator" name="Realigner Target Creator" version="0.0.3">
+<tool id="gatk2_realigner_target_creator" name="Realigner Target Creator" version="0.0.4">
   <description>for use in local realignment</description>
   <requirements>
       <requirement type="package" version="2.1">gatk</requirement>
--- a/unified_genotyper.xml	Thu Sep 20 12:03:32 2012 -0400
+++ b/unified_genotyper.xml	Thu Sep 20 13:23:44 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_unified_genotyper" name="Unified Genotyper" version="0.0.3">
+<tool id="gatk2_unified_genotyper" name="Unified Genotyper" version="0.0.4">
   <description>SNP and indel caller</description>
   <requirements>
       <requirement type="package" version="2.1">gatk</requirement>
--- a/variant_annotator.xml	Thu Sep 20 12:03:32 2012 -0400
+++ b/variant_annotator.xml	Thu Sep 20 13:23:44 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_variant_annotator" name="Variant Annotator" version="0.0.3">
+<tool id="gatk2_variant_annotator" name="Variant Annotator" version="0.0.4">
   <description></description>
   <requirements>
       <requirement type="package" version="2.1">gatk</requirement>
--- a/variant_apply_recalibration.xml	Thu Sep 20 12:03:32 2012 -0400
+++ b/variant_apply_recalibration.xml	Thu Sep 20 13:23:44 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_variant_apply_recalibration" name="Apply Variant Recalibration" version="0.0.3">
+<tool id="gatk2_variant_apply_recalibration" name="Apply Variant Recalibration" version="0.0.4">
   <description></description>
   <requirements>
       <requirement type="package" version="2.1">gatk</requirement>
--- a/variant_combine.xml	Thu Sep 20 12:03:32 2012 -0400
+++ b/variant_combine.xml	Thu Sep 20 13:23:44 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_variant_combine" name="Combine Variants" version="0.0.3">
+<tool id="gatk2_variant_combine" name="Combine Variants" version="0.0.4">
   <description></description>
   <requirements>
       <requirement type="package" version="2.1">gatk</requirement>
--- a/variant_eval.xml	Thu Sep 20 12:03:32 2012 -0400
+++ b/variant_eval.xml	Thu Sep 20 13:23:44 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_variant_eval" name="Eval Variants" version="0.0.3">
+<tool id="gatk2_variant_eval" name="Eval Variants" version="0.0.4">
   <description></description>
   <requirements>
       <requirement type="package" version="2.1">gatk</requirement>
--- a/variant_filtration.xml	Thu Sep 20 12:03:32 2012 -0400
+++ b/variant_filtration.xml	Thu Sep 20 13:23:44 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_variant_filtration" name="Variant Filtration" version="0.0.3">
+<tool id="gatk2_variant_filtration" name="Variant Filtration" version="0.0.4">
   <description>on VCF files</description>
   <requirements>
       <requirement type="package" version="2.1">gatk</requirement>
--- a/variant_recalibrator.xml	Thu Sep 20 12:03:32 2012 -0400
+++ b/variant_recalibrator.xml	Thu Sep 20 13:23:44 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_variant_recalibrator" name="Variant Recalibrator" version="0.0.3">
+<tool id="gatk2_variant_recalibrator" name="Variant Recalibrator" version="0.0.4">
   <description></description>
   <requirements>
       <requirement type="package" version="2.1">gatk</requirement>
--- a/variant_select.xml	Thu Sep 20 12:03:32 2012 -0400
+++ b/variant_select.xml	Thu Sep 20 13:23:44 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_variant_select" name="Select Variants" version="0.0.3">
+<tool id="gatk2_variant_select" name="Select Variants" version="0.0.4">
   <description>from VCF files</description>
   <requirements>
       <requirement type="package" version="2.1">gatk</requirement>
@@ -513,7 +513,7 @@
   <help>
 **What it does**
 
-Often, a VCF containing many samples and/or variants will need to be subset in order to facilitate certain analyses (e.g. comparing and contrasting cases vs. controls; extracting variant or non-variant loci that meet certain requirements, displaying just a few samples in a browser like IGV, etc.). SelectVariants can be used for this purpose. Given a single VCF file, one or more samples can be extracted from the file (based on a complete sample name or a pattern match). Variants can be further selected by specifying criteria for inclusion, i.e. "DP &gt; 1000" (depth of coverage greater than 1000x), "AF &lt; 0.25" (sites with allele frequency less than 0.25). These JEXL expressions are documented in the Using JEXL expressions section (http://www.broadinstitute.org/gsa/wiki/index.php/Using_JEXL_expressions). One can optionally include concordance or discordance tracks for use in selecting overlapping variants. 
+Often, a VCF containing many samples and/or variants will need to be subset in order to facilitate certain analyses (e.g. comparing and contrasting cases vs. controls; extracting variant or non-variant loci that meet certain requirements, displaying just a few samples in a browser like IGV, etc.). SelectVariants can be used for this purpose. Given a single VCF file, one or more samples can be extracted from the file (based on a complete sample name or a pattern match). Variants can be further selected by specifying criteria for inclusion, i.e. "DP &gt; 1000" (depth of coverage greater than 1000x), "AF &lt; 0.25" (sites with allele frequency less than 0.25). These JEXL expressions are documented in the `Using JEXL expressions section &lt;http://gatkforums.broadinstitute.org/discussion/1255/what-are-jexl-expressions-and-how-can-i-use-them-with-the-gatk&gt;`_. One can optionally include concordance or discordance tracks for use in selecting overlapping variants. 
 
 For more information on using the SelectVariants module, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_SelectVariants.html&gt;`_.
 
--- a/variants_validate.xml	Thu Sep 20 12:03:32 2012 -0400
+++ b/variants_validate.xml	Thu Sep 20 13:23:44 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_validate_variants" name="Validate Variants" version="0.0.3">
+<tool id="gatk2_validate_variants" name="Validate Variants" version="0.0.4">
   <description></description>
   <requirements>
       <requirement type="package" version="2.1">gatk</requirement>