# HG changeset patch
# User elixir-it
# Date 1541764384 18000
# Node ID 91abc25944cf2d04ef2d669b1a9bc449ec9c0300
# Parent 733c164f2759898f2173b255bc9b9e9741a1078d
Uploaded
diff -r 733c164f2759 -r 91abc25944cf covacs_VariantRecalibrator.xml
--- a/covacs_VariantRecalibrator.xml Fri Nov 09 06:52:10 2018 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,223 +0,0 @@
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- GATK VariantRecalibrator wrapper Version = 3.8
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- bed_macros.xml
- vcf_macros.xml
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- gatk
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- $log
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-.. class:: warningmark
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-**IMPORTANT** to get the wrapper ready to start the admin user have to download gatk GATK version 3.8 from the broadinstitute site https://software.broadinstitute.org/gatk/download/archive and then move it in the conda_prefix folder, the path of the conda_prefix is written in the galaxy.ini(or .yml) file
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- **more informations** at https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_variantrecalibration_VariantRecalibrator.php
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------
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-**Implemented options** VariantRecalibrator:
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-**-L** : One or more genomic intervals over which to operate(file.bed)
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-**-ip** Amount of padding (in bp) to add to each interval
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-**--resource:NAME,known=true/false,training=true/false,truth=true/false,prior=float $file** :A list of sites for which to apply a prior probability of being correct but which aren't used by the algorithm (training and truth sets are required to run)
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-**-mode** : Recalibration mode to employ (SNP|INDEL)
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-**-an** : annotations which should used for calculations
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-**-tranche** The levels of truth sensitivity at which to slice the data. (in percent, that is 1.0 for 1 percent)
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-**in case of indels mode**
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-**--minNumBadVariants** : Minimum number of bad variants
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-**--maxGaussians** : Max number of Gaussians for the positive model
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-**-mNG** : Max number of Gaussians for the negative model
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-**OUTPUTS**
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--recalFile
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--tranchesFile
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------
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-.. class:: infomark
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-**Recommended CoVaCS command**
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-**-ip** 100
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-**-R** genome.fa
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-**-input** VCF
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-**-resource**:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap.vcf
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-**-resource**:omni,known=false,training=true,truth=true,prior=12.0 omni.vcf
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-**-resource**:1000G,known=false,training=false,truth=false,prior=8.0 1000G.vcf
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-**-resource**:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp.vcf
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-**-mode** SNP
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-**-an** DP **-an** QD **-an** MQ **-an** MQRankSum **-an** ReadPosRankSum **-an** FS
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-**-tranche** 100.0 **-tranche** 99.5 **-tranche** 99.0 **-tranche** 98.5 **-tranche** 90.0
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- 10.1186/s12864-018-4508-1
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diff -r 733c164f2759 -r 91abc25944cf tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri Nov 09 06:53:04 2018 -0500
@@ -0,0 +1,17 @@
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