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1 <tool id="intersect_snp" name="intersect_snp" version="0">
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2 <description>tool for snp VCF file intersection </description>
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3 <requirements>
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4 </requirements>
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5 <command>
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6 perl $__tool_directory__/14_june_18_intersect.snps.with.infos.pl
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7 $input1 $input2 $input3 intersect 2>log
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8 </command>
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9 <inputs>
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10 <param name="input1" format="vcf" type="data" label="VCF File" help="Varscan2 snp output" />
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11 <param name="input2" format="vcf" type="data" label="VCF File" help="Frebayes snp output" />
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12 <param name="input3" format="vcf" type="data" label="VCF File" help="GATK HaplotypeCaller snp output" />
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13 </inputs>
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14 <outputs>
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15 <data format="vcf" name="output1" from_work_dir="intersect.common.snps.vcf" label="${tool.name} on ${on_string} common snps" />
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16 <data format="vcf" name="output2" from_work_dir="intersect.unique.snps.vcf" label="${tool.name} on ${on_string} unique snps" />
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17 <data format="txt" name="output3" from_work_dir="log" label="${tool.name} on ${on_string} log" />
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18 </outputs>
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19 <stdio>
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20 </stdio>
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21 <help>
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22 **WHAT IT DOES**
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23
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24 Predictions of SNPs from Varscan2, GATK and Freebayes are consolidated into a single call-set following a simple majority consensus rule. Variants identified by at least two methods are incorporated into a final “high confidence” call set.Singleton variants predicted by only one method are considered less reliable and are included in a low quality call-set.
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25
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26 **The final output consists in two VCF files:**
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27
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28 -SNPs common to at least 2 methods
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29
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30 -Singleton SNPs obtained from a single method
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31
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32 </help>
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33 <citations>
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34 <citation type="doi">10.1186/s12864-018-4508-1</citation>
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35 </citations>
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36 <tests>
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37 <test>
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38 </test>
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39 </tests>
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40
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41 </tool>
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