Mercurial > repos > yusuf > triage_rare_genotypes

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author Yusuf Ali <ali@yusuf.email>
date Wed, 25 Mar 2015 13:44:41 -0600
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1 <?xml version="1.0"?>
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2
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3 <tool id="hgvs_combine_1" name="Triage cohort rare/novel variants">
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4 <description>from combined cohort HGVS table</description>
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5 <version_string>rare_triage -v</version_string>
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6 <command interpreter="perl">rare_triage $input_hgvs_table $output_novel_gene_table $output_rare_gene_table $rare_freq $long_gene_threshold $non_coding
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8
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9 </command>
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10 <inputs>
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11 <param format="achri_snp_table" name="input_hgvs_table" type="data" label="A combined, non-collapsed HGVS annotation table for a cohort, with the sample names in the last column"/>
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12 <param name="rare_freq" type="float" value="0.001" min="0" max="1" label="Max. minor allele frequency" help=" for reporting homozygous 'rare' variants"/>
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13 <param name="long_gene_threshold" type="integer" value="30000" label="Gene length threshold" help="for making 'Exceptionally long gene' marginal cohort call"/>
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14 <param name="non_coding" type="boolean" truevalue="true" falsevalue="false" value="False" label="Report non-coding variants as well?"/>
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15 </inputs>
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16 <outputs>
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17 <data format="tabular" name="output_novel_gene_table" type="data" label="Table of novel cohort variants"/>
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18 <data format="tabular" name="output_rare_gene_table" type="data" label="Table of rare/marginal call cohort variants"/>
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19 </outputs>
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20
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21 <tests>
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22 </tests>
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23
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24 <help>
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25 This tool takes a combined HGVS table of genotype calls for a cohort, and generates two tables. The first lists genes with novel homozygous variants in all samples, allowing for locus heterogeneity. The second table lists genes with marginal calls (e.g. lots of genotyping caveats), or very rare minor allele frequencies in the general population.
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26 </help>
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27
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28 </tool>