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diff GATK/gatk/generation/gatk.xsldb.xml @ 2:2c7824a8d764 draft

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author scisjnu123
date Thu, 12 Sep 2019 06:50:21 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/generation/gatk.xsldb.xml	Thu Sep 12 06:50:21 2019 -0400
@@ -0,0 +1,57 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<analyses>
+    <analysis>
+	    <name>RealignerTargetCreator</name>
+	    <input_type>bam</input_type>
+	    <tag>rtc</tag>
+	    <macro_file>realigner_target_creator.xml</macro_file>
+    </analysis>
+    <analysis>
+	    <name>IndelRealigner</name>
+	    <input_type>bam</input_type>
+	    <tag>ir</tag>
+	    <macro_file>indel_realigner.xml</macro_file>
+    </analysis>
+    <analysis>
+	    <name>BaseRecalibrator</name>
+	    <input_type>bam</input_type>
+	    <tag>br</tag>
+	    <macro_file>base_recalibrator.xml</macro_file>
+    </analysis>
+    <analysis>
+	    <name>AnalyzeCovariates</name>
+	    <input_type>bam</input_type>
+	    <tag>ac</tag>
+	    <macro_file>analyze_covariates.xml</macro_file>
+    </analysis>
+    <analysis>
+	    <name>PrintReads</name>
+	    <input_type>bam</input_type>
+	    <tag>pr</tag>
+	    <macro_file>print_reads.xml</macro_file>
+    </analysis>
+    <analysis>
+	    <name>HaplotypeCaller</name>
+	    <input_type>bam</input_type>
+	    <tag>hc</tag>
+	    <macro_file>haplotype_caller.xml</macro_file>
+    </analysis>
+    <analysis>
+	    <name>GenotypeGVCFs</name>
+	    <input_type>gvcf</input_type>
+	    <tag>gg</tag>
+	    <macro_file>genotype_gvcfs.xml</macro_file>
+    </analysis>
+    <analysis>
+	    <name>CombineGVCFs</name>
+	    <input_type>gvcf</input_type>
+	    <tag>cg</tag>
+	    <macro_file>combine_gvcfs.xml</macro_file>
+    </analysis>
+    <analysis>
+	    <name>CombineVariants</name>
+	    <input_type>vcf</input_type>
+	    <tag>cv</tag>
+	    <macro_file>combine_variants.xml</macro_file>
+    </analysis>
+</analyses>