diff ConcordanceReport.xml @ 0:2d601bd04c93 default tip

initial commit

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ConcordanceReport.xml	Wed Mar 25 13:28:12 2015 -0600
@@ -0,0 +1,32 @@
+<?xml version="1.0"?>
+
+<tool id="concordance_report_1" name="Compute intra-NGS concordance">
+  <description>over targeted regions in a genome</description>
+  <version_string>kappa_report -v</version_string>
+  <command interpreter="perl">kappa_report -q $target_bed $coding_gtf $input_ngs_calls1 $input_bam1 $coverage_cutoff1 $input_ngs_calls2 $input_bam2 $coverage_cutoff2 $out_summary_table</command>
+  <inputs>
+    <param format="gtf" name="coding_gtf" type="data" label="Coding regions" help="This must be the same (GTF) file used to define the coding regions for the HGVS annotation of the NGS variant calls"/>
+    <param format="bed" name="target_bed" type="data" label="Target sequencing regions" help="e.g. a BED file from the Shared Data 'Exome target regions' folder, corresponding to the capture kit used for sequencing the sample"/>
+    <param format="achri_snp_table" name="input_ngs_calls1" type="data" label="HGVS annotated NGS variant calls for genotyping method #1"/>
+    <param format="bam" name="input_bam1" type="data" label="Mapped reads file (BAM) that was used to generate the NGS variant calls for genotyping method #1"/>
+    <param type="integer" name="coverage_cutoff1" value="20" min="1" max="40" label="Report method #1 calls only for positions with read depth equal to or greater than..."/>
+    <param format="achri_snp_table" name="input_ngs_calls2" type="data" label="HGVS annotated NGS variant calls for genotyping method #2"/>
+    <param format="bam" name="input_bam2" type="data" label="Mapped reads file (BAM) that was used to generate the NGS variant calls for genotyping method #2"/>
+    <param type="integer" name="coverage_cutoff2" value="20" min="1" max="40" label="Report method #2 calls only for positions with read depth equal to or greater than..."/>
+  </inputs>
+  <outputs>
+    <data name="out_summary_table" format="tabular" label="Concordance summary (shared, unique calls, etc.)"/>
+  </outputs>
+
+  <tests>
+  </tests>
+
+  <help>
+**What it does**
+
+This tool reports several statistics comparing the genotypes derived from two next-gen sequencing runs. This is intended to measure methodological consistency,
+assuming the samples for both methods are from the same individual. When coverage is good (typically 10x for colorspace, 20x for base space), there should be a large
+(>= 95%) overlap between the calls if they are reasonably accurate.
+  </help>
+
+</tool>