Mercurial > repos > artbio > lumpy_smoove

annotate lumpy_smoove.xml @ 3:65b400409455 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
author artbio
date Wed, 26 Aug 2020 12:24:07 -0400
parents 49a8a327cc72
children 49da975ba395
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3
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
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1 <tool id="lumpy_smoove" name="lumpy_smoove" version="0.5.0">
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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2 <description>find structural variants using the smoove workflow</description>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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3 <macros>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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4 <import>macro_lumpy_smoove.xml</import>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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5 </macros>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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6 <requirements>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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7 <requirement type="package" version="0.2.5">smoove</requirement>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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8 </requirements>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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9 <stdio>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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10 <exit_code range="1:" level="fatal" description="Tool exception" />
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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11 </stdio>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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12 <command detect_errors="exit_code"><![CDATA[
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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13 @pipefail@
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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14 @set_fasta_index@
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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15 ln -s $normal_bam normal.bam &&
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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16 ln -s $tumor_bam tumor.bam &&
3
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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17 samtools index -@ \${GALAXY_SLOTS:-4} normal.bam &&
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
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18 samtools index -@ \${GALAXY_SLOTS:-4} tumor.bam &&
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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19
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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20 smoove call --name output
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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21 #if $set_exclusion.choices=="yes":
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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22 --exclude $bedmask
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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23 #end if
3
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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24 --fasta reference.fa
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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25 --processes \${GALAXY_SLOTS:-4}
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
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26 --genotype
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
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27 #if $prpos=="no":
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
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28 --removepr
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
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29 #end if
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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30 normal.bam tumor.bam &&
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
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31 ls -latr &&
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
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32 gunzip output-smoove.genotyped.vcf.gz
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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33
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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34 ]]></command>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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35 <inputs>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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36 <expand macro="reference_source_conditional" />
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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37 <param format="bam" name="normal_bam" type="data" label="BAM alignments from the normal sample"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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38 <param format="bam" name="tumor_bam" type="data" label="BAM alignments from the tumor sample"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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39 <conditional name="set_exclusion">
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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40 <param name="choices" type="select" label="exclude regions with a bed file" display="radio">
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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41 <option value="no" selected="true">No</option>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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42 <option value="yes">Yes</option>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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43 </param>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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44 <when value="yes">
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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45 <param format="bed" name="bedmask" type="data" label="BED regions to be excluded for the analysis"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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46 </when>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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47 <when value="no">
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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48 </when>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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49 </conditional>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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50 <param name="prpos" type="select" label="include the PRPOS probabilities in INFO tags" display="radio">
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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51 <option value="no" selected="true">No</option>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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52 <option value="yes">Yes</option>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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53 </param>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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54 </inputs>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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55
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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56 <outputs>
3
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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57 <data format="vcf" name="vcf_call" label="lumpy-smoove Variant Calling" from_work_dir="./output-smoove.genotyped.vcf" />
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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58 </outputs>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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59
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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60 <tests>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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61 <test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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62 <param name="reference_source_selector" value="history" />
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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63 <param name="ref_file" value="chrI-ce11.fa"/>
3
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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64 <param name="normal_bam" value="celegans_RG_1.bam"/>
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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65 <param name="tumor_bam" value="celegans_RG_2.bam"/>
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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66 <param name="choices" value="yes"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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67 <param name="bedmask" value="exclude.bed"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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68 <param name="prpos" value="no"/>
3
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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69 <output name="vcf_call" ftype="vcf" file="result-1.vcf" lines_diff="6"/>
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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70 </test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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71 <test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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72 <param name="reference_source_selector" value="history" />
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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73 <param name="ref_file" value="chrI-ce11.fa"/>
3
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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74 <param name="normal_bam" value="celegans_RG_1.bam"/>
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
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75 <param name="tumor_bam" value="celegans_RG_2.bam"/>
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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76 <param name="choices" value="no"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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77 <param name="prpos" value="no"/>
3
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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78 <output name="vcf_call" ftype="vcf" file="result-2.vcf" lines_diff="6"/>
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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79 </test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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80 <test>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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81 <param name="reference_source_selector" value="history" />
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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82 <param name="ref_file" value="chrI-ce11.fa"/>
3
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
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83 <param name="normal_bam" value="celegans_RG_2.bam"/>
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
artbio
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84 <param name="tumor_bam" value="celegans_RG_1.bam"/>
0
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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85 <param name="choices" value="no"/>
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
artbio
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86 <param name="prpos" value="no"/>
3
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87 <output name="vcf_call" ftype="vcf" file="result-3.vcf" lines_diff="6"/>
0
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88 </test>
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89 <test>
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90 <param name="reference_source_selector" value="history" />
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91 <param name="ref_file" value="chrI-ce11.fa"/>
3
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92 <param name="normal_bam" value="celegans_RG_1.bam"/>
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93 <param name="tumor_bam" value="celegans_RG_2.bam"/>
0
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94 <param name="choices" value="no"/>
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95 <param name="prpos" value="yes"/>
3
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96 <output name="vcf_call" ftype="vcf" file="result-4.vcf" lines_diff="6"/>
0
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97 </test>
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98
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99 </tests>
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100
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101 <help>
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102 **smoove** simplifies and speeds calling and genotyping SVs for short reads. It also improves
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103 specificity by removing many spurious alignment signals that are indicative of low-level
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104 noise and often contribute to spurious calls.
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105
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106 There is a blog-post describing smoove in more detail
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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107 here: https://brentp.github.io/post/smoove/
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108
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109 Currently, this Galaxy tool only wraps smoove for 2 samples (bam normal and tumor inputs),
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110 which translates in the command line::
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111
3
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112 <![CDATA[smoove call --name my-cohort --exclude $bed --fasta $fasta -p $threads --genotype [--removepr] /path/to/*.bam]]>
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113
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114
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115 the --exclude $bed is highly recommended as it can be used to ignore reads that overlap
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116 problematic regions.
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117
3
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118 A good set of regions for GRCh37 can be found here_
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119
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120 .. _here: https://github.com/hall-lab/speedseq/blob/master/annotations/ceph18.b37.lumpy.exclude.2014-01-15.bed
65b400409455 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit c52939d44f8e8287ad4068949daadf616879f008"
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121
0
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122
3
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123 And a good set for GRCh38 can be found there_
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124
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125 .. _there: https://github.com/hall-lab/speedseq/blob/master/annotations/exclude.cnvnator_100bp.GRCh38.20170403.bed
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126
0
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127
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128 smoove will::
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129
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130 1. parallelize calls to lumpy_filter to extract split and discordant reads required by lumpy
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131
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132 2. further filter lumpy_filter calls to remove high-coverage, spurious regions and user-specified chroms like 'hs37d5';
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133 it will also remove reads that we've found are likely spurious signals. after this, it will
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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134 remove singleton reads (where the mate was removed by one of the previous filters)
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135 from the discordant bams. This makes lumpy much faster and less memory-hungry.
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136
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137 3. calculate per-sample metrics for mean, standard deviation, and distribution of insert
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138 size as required by lumpy.
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139
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140 4. stream output of lumpy directly into multiple svtyper processes for parallel-by-region
3
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141 genotyping while lumpy is still running.
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142
3
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143 5. sort, compress, and index final VCF (but this galaxy wrapper is uncompression the gzip_vcf output)
0
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144
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145 **Input(s)**
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146
3
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147 * BAM files: One Bam for normal sample and one Bam for tumor sample. Only BAM alignments produced by BWA-mem have been tested with this tool
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148
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149 .. class:: warningmark
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150
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151 It is mandatory for proper run of svtyper that **BAM files contain read group information**,
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152 ie the @RG tag is present and filled in each BAM
0
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153
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154
3
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155 * A bed file describing the regions to exclude from the analysis
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156 * Additional options*: refer to smoove GitHub repository_ and the lumpy publication (doi 10.1186/gb-2014-15-6-r84)
0
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157
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158 .. _repository: https://github.com/brentp/smoove
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159
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160
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161 Options::
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162
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163 <![CDATA[
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164
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165 smoove calls several programs. Those with 'Y' are found on your $PATH. Only those with '*' are required.
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166
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167 [Y] bgzip [ sort -> (compress) -> index ]
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168 [Y] gsort [(sort) -> compress -> index ]
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169 [Y] tabix [ sort -> compress -> (index)]
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170 [Y] lumpy
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171 [Y] lumpy_filter
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172 [Y] samtools
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173 [Y] svtyper
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174 [Y] mosdepth [extra filtering of split and discordant files for better scaling]
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175
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176 [Y] duphold [(optional) annotate calls with depth changes]
ee8fc44b1655 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
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177 [Y] svtools [only needed for large cohorts].
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178
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179 Available sub-commands are below. Each can be run with -h for additional help.
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180
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181 call : call lumpy (and optionally svtyper)
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182 merge : merge and sort (using svtools) calls from multiple samples
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183 genotype : parallelize svtyper on an input VCF
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184 paste : square final calls from multiple samples (each with same number of variants)
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185 plot-counts : plot counts of split, discordant reads before, after smoove filtering
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186 annotate : annotate a VCF with gene and quality of SV call
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187 hipstr : run hipSTR in parallel
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188 cnvnator : run cnvnator in parallel
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189 duphold : run duphold in parallel (this can be done by adding a flag to call or genotype)
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190 ]]>
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191 </help>
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192
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193 <citations>
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194 <citation type="doi">10.1186/gb-2014-15-6-r84</citation>
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195 </citations>
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196 </tool>