# HG changeset patch
# User elixir-it
# Date 1541761408 18000
# Node ID 6d8aa1176a94e29f271fef020f617974789d3465
Uploaded
diff -r 000000000000 -r 6d8aa1176a94 covacs_Select_Filtration.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/covacs_Select_Filtration.xml Fri Nov 09 06:03:28 2018 -0500
@@ -0,0 +1,75 @@
+
+ SelectVariants VariantFiltration wrapper for covacs, use in case of not enough snp or indels error in covacs_VariantRecalibrator
+
+
+
+ gatk
+
+
+ $log
+ &&
+ java -jar \$CONDA_PREFIX/../../GenomeAnalysisTK.jar
+ -T VariantFiltration
+ -R $ref_file.fields.path
+ -V variants_recal.indels.vcf
+ --filterExpression "DP<8 || QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0"
+ --filterName "filter_LQ_$TYPE"
+ -o variants_recal.filtered.small.panel.region.vcf
+
+ 2>> $log
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ **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
+
+ **more informations** at https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php , https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_filters_VariantFiltration.php
+
+**Implemented options** SelectVariants VariantFiltration
+
+-R Reference sequence file
+
+-V vcf input
+
+other options are fixed based on covacs pipeline
+
+**description** this step can be used if covacs_indel_snp have not enough data to create the model, it calls SelectVariants and VariantFiltration applying the filter expression --filterExpression 200.0 || ReadPosRankSum < -20.0"]]> to filter the variants both snp and indels
+
+
+
+ 10.1186/s12864-018-4508-1
+
+
+
diff -r 000000000000 -r 6d8aa1176a94 mv_untar_gatk.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mv_untar_gatk.sh Fri Nov 09 06:03:28 2018 -0500
@@ -0,0 +1,9 @@
+#!/bin/bash
+#if the .jar file is not present in the conda_prefix the script search the tar.gz in the conda_prefix of the vm
+#and untar the archive
+if [[ ! -f $CONDA_PREFIX/../../GenomeAnalysisTK.jar ]] ; then
+ tar -zxvf $CONDA_PREFIX/../../GenomeAnalysis*.tar.gz -C $CONDA_PREFIX/../../
+
+else
+ echo GATK is present
+fi
diff -r 000000000000 -r 6d8aa1176a94 tool-data/covacs_gatk_indexes.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/covacs_gatk_indexes.loc.sample Fri Nov 09 06:03:28 2018 -0500
@@ -0,0 +1,36 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of all covacs wrapper that need a gatk reference. You will need
+#to create these data files and then create a covacs_gatk_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The covacs_gatk_indexes.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#
+#
+#So, for example, if you had phiX indexed stored in
+#/depot/data2/galaxy/phiX/base/,
+#then the bwa_index.loc entry would look like this:
+#
+#phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa
+#
+#and your /depot/data2/galaxy/phiX/base/ directory
+#would contain phiX.dict, phiX.fa.fai files.
+#
+#
+#Your covacs_gatk_indexes.loc file should include an entry per line for each
+#index set you have stored. The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files. For example:
+#
+#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa
+#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa
+#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa
+#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa
+#...etc...
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#
+hg38 hg38 hg38_GDC /export/gatkhg38pl/GRCh38.d1.vd1.fa
+hg19 hg19 hg19 /export/gatk_hg19_index_bundle/ucsc.hg19.fasta
diff -r 000000000000 -r 6d8aa1176a94 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 06:03:28 2018 -0500
@@ -0,0 +1,12 @@
+
+
+