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1 <tool id="snpSift_filter" name="SnpSift Filter" version="3.1">
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2 <options sanitize="False" />
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3 <description>Filter variants using arbitrary expressions</description>
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4 <!--
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5 You will need to change the path to wherever your installation is.
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6 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
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7 java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output
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8 -->
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9 <requirements>
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10 <requirement type="package" version="3.1">snpEff</requirement>
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11 </requirements>
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12 <command>
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13 java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output
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14 </command>
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15 <inputs>
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16 <param format="vcf" name="input" type="data" label="VCF input"/>
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17 <param name="expr" type="text" label="Expression" size="50"/>
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18 </inputs>
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19 <configfiles>
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20 <configfile name="exprFile">
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21 $expr
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22 </configfile>
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23 </configfiles>
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24
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25 <outputs>
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26 <data format="vcf" name="output" />
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27 </outputs>
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28 <stdio>
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29 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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30 <exit_code range="1:" level="fatal" description="Error" />
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31 </stdio>
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32 <help>
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33
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1
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34 **SnpSift filter**
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35
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36 You can filter ia vcf file using arbitrary expressions, for instance "(QUAL > 30) | (exists INDEL) | ( countHet() > 2 )". The actual expressions can be quite complex, so it allows for a lot of flexibility.
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37
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38 Some examples:
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39
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40 - *I want to filter out samples with quality less than 30*:
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41
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42 * **( QUAL > 30 )**
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43
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44 - *...but we also want InDels that have quality 20 or more*:
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45
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46 * **(( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )**
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47
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1
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48 - *...or any homozygous variant present in more than 3 samples*:
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49
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50 * **(countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )**
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51
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52 - *...or any heterozygous sample with coverage 25 or more*:
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53
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54 * **((countHet() > 0) && (DP >= 25)) | (countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )**
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55
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56 - *I want to keep samples where the genotype for the first sample is homozygous variant and the genotype for the second sample is reference*:
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57
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58 * **isHom( GEN[0] ) & isVariant( GEN[0] ) & isRef( GEN[1] )**
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59
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60
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61 For complete details about this tool and epressions that can be used, please go to http://snpeff.sourceforge.net/SnpSift.html#filter
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62
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63 </help>
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64 </tool>
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