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1 <?xml version="1.0"?>
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2
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3 <tool id="microarray_reports_1" name="Compute NGS/microarray concordance">
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4 <description>over targeted regions in a genome</description>
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5 <version_string>microarray_reports -v</version_string>
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6 <command interpreter="perl">microarray_reports $__tool_data_path__ -q $out_discordant_bed $out_summary_table $input_ngs_calls $input_micro_calls $input_bam $target_gtf $ref_genome.fa $coverage_cutoff $target_bed</command>
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7 <inputs>
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8 <param format="achri_snp_table" name="input_ngs_calls" type="data" label="HGVS annotated NGS variant calls"/>
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9 <param format="tabular" name="input_micro_calls" type="data" label="Microarray genotype calls. See help info below this form for required input format."/>
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10 <param format="bam" name="input_bam" type="data" label="Mapped reads file (BAM) that was used to generate the NGS variant calls"/>
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11 <param type="integer" name="coverage_cutoff" value="9" min="0" max="40" label="Report only positions with read depth greater than..."/>
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12 <param name="ref_genome" type="genomebuild" label="Reference genome" help="against which the NGS variants were called"/>
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13 <param format="gtf" name="target_gtf" type="data" label="Target regions" help="This must be the same (GTF) file used to define the coding regions for the HGVS annotation of the NGS variant calls"/>
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14 <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 the
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15 to the capture kit used for sequencing the sample"/>
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16 </inputs>
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17 <outputs>
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18 <data name="out_summary_table" format="tabular" label="Concordance summary (false positive rate, etc.)"/>
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19 <data name="out_discordant_bed" format="bed" label="Discordant call locations"/>
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20 </outputs>
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21
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22 <tests>
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23 </tests>
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24
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25 <help>
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26 **What it does**
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27
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28 This tool reports several statistics comparing the genotypes derived from a next-gen sequencing run to a microarray genotyping result
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29 for the same individual. When coverage is good (10x for colorspace, 20x for base space), false positive and false negative rates should
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30 be below 2%, assuming 99% accuracy of both the microarray and the NGS genotyping.
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31
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32 ------
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33
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34 ** Example**
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35
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36 The microarray file should have five columns (ProbeID, forward strand genotypes, dbSNP ID, chr, pos), e.g.::
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37
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38 #Comment lines...
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39 Probe set header line
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40 SNP_A-1780520 GG rs16994928 20 48440771
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41 SNP_A-1780985 AG rs3859360 18 34178190
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42 </help>
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43
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44 </tool>
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