Mercurial > repos > yusuf > concordance_report
comparison ConcordanceReport.xml @ 0:2d601bd04c93 default tip
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author | Yusuf Ali <ali@yusuf.email> |
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date | Wed, 25 Mar 2015 13:28:12 -0600 |
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1 <?xml version="1.0"?> | |
2 | |
3 <tool id="concordance_report_1" name="Compute intra-NGS concordance"> | |
4 <description>over targeted regions in a genome</description> | |
5 <version_string>kappa_report -v</version_string> | |
6 <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> | |
7 <inputs> | |
8 <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"/> | |
9 <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"/> | |
10 <param format="achri_snp_table" name="input_ngs_calls1" type="data" label="HGVS annotated NGS variant calls for genotyping method #1"/> | |
11 <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"/> | |
12 <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..."/> | |
13 <param format="achri_snp_table" name="input_ngs_calls2" type="data" label="HGVS annotated NGS variant calls for genotyping method #2"/> | |
14 <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"/> | |
15 <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..."/> | |
16 </inputs> | |
17 <outputs> | |
18 <data name="out_summary_table" format="tabular" label="Concordance summary (shared, unique calls, etc.)"/> | |
19 </outputs> | |
20 | |
21 <tests> | |
22 </tests> | |
23 | |
24 <help> | |
25 **What it does** | |
26 | |
27 This tool reports several statistics comparing the genotypes derived from two next-gen sequencing runs. This is intended to measure methodological consistency, | |
28 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 | |
29 (>= 95%) overlap between the calls if they are reasonably accurate. | |
30 </help> | |
31 | |
32 </tool> |