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1 <tool id="snvmix_somatic_filter" name="Get somatic positions from germline SNVMix output" version="0.12.1-rc1">
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2 <requirements>
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3 <requirement type="package">SNVMix</requirement>
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4 </requirements>
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5 <description>Takes SNVMix output from a set of specific sites in a bam file from a matched normal sample and the SNV calls from the tumour to identify and report high-confidence somatic mutations</description>
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6 <command interpreter="python">
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7 filter_snvmix_somatic.py
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8 -n $input1
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9 -t $input2
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10 -o $output1
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11 -p $posterior
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12 -d $nonref_support
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13 </command>
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14 <inputs>
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15 <param name="input1" type="data" format="tabular" label="Select the SNVMix raw output from your normal library" />
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16 <param name="input2" type="data" format="tabular" label="Select the annotated SNV calls from your tumour library" />
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17 <param name="posterior" type="float" value="0.999" label="Choose a minimum value for the reference state posterior probability p(AA)" />
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18 <param name="nonref_support" type="integer" value="2" label="Choose a maximum number of non-reference base calls allowed at a site" />
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19 </inputs>
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20 <outputs>
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21 <data format="tabular" name="output1" label="${tool.name}: Somatic positions" />
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22 </outputs>
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23 <help>
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24
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25 **What it does**
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26 Takes the positions identified as SNVs by SNVMix in a tumour sample and compares them to raw SNVMix output from the matched "normal" sequence from the same individual.
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27 The input from the normal must have run SNVMix with the -f (full) option ("SNVMix at selected positions" tool).
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28 The -p option (posterior) is then used to retain only the variants with a strong posterior probability of being "reference" at each position.
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29 These are the high-confidence somatic SNV calls. Variants can be further thresholded for enhanced stringency using the -d (nonref_support) option.
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30 If more than -d non-reference reads exist at the site, the SNV is also considered a "germ line" event and not reported as somatic. This process returns
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31 only the sites that can be confidently identified as somatic. Thus, with limiting or no coverage at the corresponding position in the germ line,
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32 some true somatic sites may not be identified.
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33
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34
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35 </help>
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36 </tool>
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