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annotate lumpy.xml @ 4:2f41fac75575 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 66d42b0d63ff5d72c6611106ed3366a58c73a55d
author drosofff
date Wed, 07 Dec 2016 09:52:03 -0500
parents 0bd777f0d6d8
children 745cbe841e40
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b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
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1 <tool id="lumpy" name="lumpy-sv" version="0.2">
0
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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2 <description>find structural variants</description>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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3 <requirements>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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4 <requirement type="package" version="0.2.12">lumpy-sv</requirement>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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5 <requirement type="package" version="1.3.1">samtools</requirement>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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6 <requirement type="package" version="1.11.2">numpy</requirement>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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7 </requirements>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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8 <stdio>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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9 <exit_code range="1:" level="fatal" description="Tool exception" />
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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10 </stdio>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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11 <version_command>lumpy --version</version_command>
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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12 <command><![CDATA[
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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13 #if $analysis_type.analysis_type_list == "one_sample":
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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14 ln -f -s $analysis_type.input_file input.bam &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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15 #else:
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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16 ln -f -s $analysis_type.input_file input.A.bam &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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17 ln -f -s $analysis_type.input_fileB input.B.bam &&
0
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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18 #end if
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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19
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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20 #if $analysis_type.analysis_type_list == "one_sample":
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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21
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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22 #if $seq_method.seq_method_list == "paired-end":
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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23 samtools view -b -F 1294 input.bam > "input.discordants.unsorted.bam" &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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24 samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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25 samtools sort input.discordants.unsorted.bam > input.discordants.bam &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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26 samtools sort input.splitters.unsorted.bam > input.splitters.bam &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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27 samtools view -r readgroup input.bam
4
2f41fac75575 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 66d42b0d63ff5d72c6611106ed3366a58c73a55d
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28 |tail -n +1
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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29 |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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30 mean=\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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31 stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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32 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
3
0bd777f0d6d8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 336e603ddd23f30f60f1cc40a4e8e1629d467055
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33 -pe id:input.bam,bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$analysis_type.readLength,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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34 -sr id:input.bam,bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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35 mv input.discordants.bam $discordants &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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36 mv input.splitters.bam $splits &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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37 mv input.lib.histo $histogram &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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38 mv output.vcf $vcf_call &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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39 rm input.discordants.unsorted.bam input.splitters.unsorted.bam meandev.txt
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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40 #end if
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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41 #if $seq_method.seq_method_list == "single-read":
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
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42 samtools view -h input.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.splitters.unsorted.bam" &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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43 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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44 -sr id:input.bam,bam_file:input.splitters.unsorted.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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45 mv input.splitters.unsorted.bam $splits &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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46 mv output.vcf $vcf_call
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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47 #end if
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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48
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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49 #else:
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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50
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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51 #if $seq_method.seq_method_list == "paired-end":
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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52 samtools view -b -F 1294 input.A.bam > "input.A.discordants.unsorted.bam" &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
drosofff
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53 samtools view -b -F 1294 input.B.bam > "input.B.discordants.unsorted.bam" &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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54 samtools view -h input.A.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.A.splitters.unsorted.bam" &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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55 samtools view -h input.B.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.B.splitters.unsorted.bam" &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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56 samtools sort input.A.discordants.unsorted.bam > input.A.discordants.bam &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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57 samtools sort input.B.discordants.unsorted.bam > input.B.discordants.bam &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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58 samtools sort input.A.splitters.unsorted.bam > input.A.splitters.bam &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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59 samtools sort input.B.splitters.unsorted.bam > input.B.splitters.bam &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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60 samtools view -r readgroup input.A.bam
4
2f41fac75575 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 66d42b0d63ff5d72c6611106ed3366a58c73a55d
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61 |tail -n +1
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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62 |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.A.lib.histo > meandevA.txt &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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63 samtools view -r readgroup input.B.bam
4
2f41fac75575 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 66d42b0d63ff5d72c6611106ed3366a58c73a55d
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64 |tail -n +1
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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65 |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.B.lib.histo > meandevB.txt &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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66 meanA=\$(cat meandevA.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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67 meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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68 stdevA=\$(cat meandevA.txt | sed -r s/mean:.+stdev://) &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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69 stdevB=\$(cat meandevB.txt | sed -r s/mean:.+stdev://) &&
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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70 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
3
0bd777f0d6d8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 336e603ddd23f30f60f1cc40a4e8e1629d467055
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71 -pe id:inputA.bam,bam_file:input.A.discordants.bam,histo_file:input.A.lib.histo,mean:"\$meanA",stdev:"\$stdevA",read_length:$analysis_type.readLength,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold
0bd777f0d6d8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 336e603ddd23f30f60f1cc40a4e8e1629d467055
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72 -pe id:inputB.bam,bam_file:input.B.discordants.bam,histo_file:input.B.lib.histo,mean:"\$meanB",stdev:"\$stdevA",read_length:$analysis_type.readLengthB,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold
2
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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73 -sr id:inputA.bam,bam_file:input.A.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold
b1e152172de9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 5f3fb85a6eb667b04c4de65eb722261f315c8241
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74 -sr id:inputB.bam,bam_file:input.B.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf &&
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75 mv input.A.discordants.bam $discordants &&
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76 mv input.B.discordants.bam $discordantsB &&
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77 mv input.A.splitters.bam $splits &&
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78 mv input.B.splitters.bam $splitsB &&
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79 mv input.A.lib.histo $histogram &&
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80 mv input.B.lib.histo $histogramB &&
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81 mv output.vcf $vcf_call &&
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82 rm input.A.discordants.unsorted.bam input.B.discordants.unsorted.bam input.A.splitters.unsorted.bam input.B.splitters.unsorted.bam meandevA.txt meandevB.txt
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83 #end if
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84 #if $seq_method.seq_method_list == "single-read":
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85 samtools view -h input.A.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.A.splitters.unsorted.bam" &&
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86 samtools view -h input.B.bam | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools view -Sb - > "input.B.splitters.unsorted.bam" &&
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87 lumpy -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
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88 -sr id:input.A.bam,bam_file:input.A.splitters.unsorted.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold
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89 -sr id:input.B.bam,bam_file:input.B.splitters.unsorted.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > output.vcf &&
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90 mv input.A.splitters.unsorted.bam $splits &&
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91 mv input.B.splitters.unsorted.bam $splitsB &&
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92 mv output.vcf $vcf_call
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93 #end if
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94
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95
0
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96 #end if
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97
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98 ]]></command>
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99 <!-- basic error handling -->
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100 <inputs>
2
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101 <conditional name="analysis_type">
3
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102 <param help="Single or paired conditions (eg tumor vs normal)" label="Input(s)" name="analysis_type_list" type="select">
2
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103 <option selected="True" value="one_sample">One Sample</option>
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104 <option value="two_sample">Two samples</option>
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105 </param>
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106 <when value="one_sample">
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107 <param format="bam" name="input_file" type="data" label="One BAM alignment file produced by BWA-mem"/>
3
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108 <param name="readLength" value="151" type="integer" label="read length" help="e.g. 151 nt" />
2
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109 </when>
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110 <when value="two_sample">
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111 <param format="bam" name="input_file" type="data" label="One BAM alignment file produced by BWA-mem"/>
3
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112 <param name="readLength" value="151" type="integer" label="read length" help="e.g. 151 nt" />
2
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113 <param format="bam" name="input_fileB" type="data" label="One BAM alignment file produced by BWA-mem"/>
3
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114 <param name="readLengthB" value="151" type="integer" label="read length" help="e.g. 151 nt" />
2
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115 </when>
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116 </conditional>
0
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117 <conditional name="seq_method">
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118 <param help="Paired-end or single-read sequencing" label="Sequencing method" name="seq_method_list" type="select">
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119 <option selected="True" value="paired-end">Paired-end sequencing</option>
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120 <option value="single-read">Single-read sequencing</option>
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121 </param>
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122 <when value="paired-end">
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123 <section name="additional_params" title="Additional Options" expanded="False">
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124 <param name="samplingValue" value="100000" type="integer" label="number of reads to compute mean and stdev of read length" help="e.g. 10000" />
2
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125 <param name="mw" value="4" type="integer" label="-mw" help="minimum weight across all samples for a call (default: 4)" />
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126 <param name="tt" value="0" type="integer" label="-tt" help="trim threshold (default: 0)" />
0
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127 <param name="min_non_overlap" value="101" type="integer" label="min_non_overlap" help="e.g. 101" />
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128 <param name="discordant_z" value="5" type="integer" label="discordant_z" help="e.g. 5" />
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129 <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" />
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130 <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" />
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131 <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" />
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132 </section>
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133 </when>
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134 <when value="single-read">
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135 <section name="additional_params" title="Additional Options" expanded="False">
2
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136 <param name="mw" value="4" type="integer" label="-mw" help="minimum weight across all samples for a call (default: 4)" />
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137 <param name="tt" value="0" type="integer" label="-tt" help="trim threshold (default: 0)" />
0
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138 <param name="back_distance" value="10" type="integer" label="back_distance" help="e.g. 10" />
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139 <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" />
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140 <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" />
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141 </section>
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142 </when>
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143
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144 </conditional>
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145
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146 </inputs>
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147
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148 <outputs>
4
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149 <data format="tabular" name="histogram" label="Lumpy on ${analysis_type.input_file.element_identifier}: Fragment size distribution">
0
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150 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
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151 </data>
4
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152 <data format="tabular" name="histogramB" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Fragment size distribution">
2
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153 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
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154 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
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155 </data>
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156 <data format="bam" name="splits" label="Lumpy on ${analysis_type.input_file.element_identifier}: Split Reads (Bam format)"/>
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157 <data format="bam" name="splitsB" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Split Reads (Bam format)">
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158 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
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159 </data>
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160 <data format="bam" name="discordants" label="Lumpy on ${analysis_type.input_file.element_identifier}: Discordant Pairs (Bam format)">
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161 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
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162 </data>
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163 <data format="bam" name="discordantsB" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Discordant Pairs (Bam format)">
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164 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
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165 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
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166 </data>
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167 <data format="vcf" name="vcf_call" label="Lumpy Variant Calling (vcf format)"/>
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168 </outputs>
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169
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170 <tests>
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171 <test>
2
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172 <param name="analysis_type" value="one_sample" />
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173 <param name="input_file" value="sr.input.bam" ftype="bam"/>
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174 <param name="seq_method_list" value="single-read" />
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175 <param name="mw" value="4"/>
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176 <param name="tt" value="0"/>
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177 <param name="back_distance" value="10"/>
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178 <param name="weight" value="1" />
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179 <param name="min_mapping_threshold" value="20" />
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180 <output name="vcf_call" file="output.vcf" ftype="vcf"/>
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181 </test>
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182 </tests>
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183
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184 <help>
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185
3
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186 **Input(s)**
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187
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188 *One sample* : lumpy search structural variations inside a single sequencing dataset
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189
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190 *Two samples*: lumpy search structural variations inside and across two sequencing datasets from two samples
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191
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192 Analysis of sample replicates is not implemented yet in this wrapper
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193
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194 *BAM files*: Only BAM alignments produced by BWA-mem have been tested with this tool
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195
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196 **Sequencing method**
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197
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198 *Paired-end sequencing*: Both ends of library fragments have been sequenced, resulting in two paired sequencing datasets
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199
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200 *Single-read sequencing*: Only one end of library fragment has been sequenced, resulting in a single sequencing dataset. Under these conditions, evidences of structural variation are obtained only from splited read alignments
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201
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202 *Read length*: The length of the sequencing reads in the library. This information is required only for paired-end sequencing data
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203
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204 *Additional options*: refer to lumpy-sv_ documentation and the publication (doi 10.1186/gb-2014-15-6-r84)
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205
1
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206 **lumpy-sv manual**
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207
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208 Read the lumpy-sv_ documentation for details on using lumpy.
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209
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210 .. _lumpy-sv: https://github.com/arq5x/lumpy-sv
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211
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212 **lumpy options**
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213
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214 v 0.2.13
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215 Author: Ryan Layer (rl6sf@virginia.edu)
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216
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217 Summary: Find structural variations in various signals.
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218
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219 Options::
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220
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221 -g Genome file (defines chromosome order)
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222 -e Show evidence for each call
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223 -w File read windows size (default 1000000)
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224 -mw minimum weight for a call
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225 -msw minimum per-sample weight for a call
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226 -tt trim threshold
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227 -x exclude file bed file
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228 -t temp file prefix, must be to a writeable directory
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229 -P output probability curve for each variant
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230 -b output BEDPE instead of VCF
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231 -sr bam_file:&lt;file name&gt;,
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232 id:&lt;sample name&gt;,
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233 back_distance:&lt;distance&gt;,
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234 min_mapping_threshold:&lt;mapping quality&gt;,
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235 weight:&lt;sample weight&gt;,
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236 min_clip:&lt;minimum clip length&gt;,
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237 read_group:&lt;string&gt;
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238
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239 -pe bam_file:&lt;file name&gt;,
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240 id:&lt;sample name&gt;,
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241 histo_file:&lt;file name&gt;,
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242 mean:&lt;value&gt;,
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243 stdev:&lt;value&gt;,
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244 read_length:&lt;length&gt;,
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245 min_non_overlap:&lt;length&gt;,
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246 discordant_z:&lt;z value&gt;,
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247 back_distance:&lt;distance&gt;,
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248 min_mapping_threshold:&lt;mapping quality&gt;,
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249 weight:&lt;sample weight&gt;,
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250 read_group:&lt;string&gt;
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251
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252 -bedpe bedpe_file:&lt;bedpe file&gt;,
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253 id:&lt;sample name&gt;,
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254 weight:&lt;sample weight&gt;
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255
0
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256 </help>
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257
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258 <citations>
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259 <citation type="doi">10.1186/gb-2014-15-6-r84</citation>
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260 </citations>
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261 </tool>