Mercurial > repos > iuc > samblaster
annotate samblaster.xml @ 3:595c942ad3ad draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 32feb54c292e406e2982f92284fb7ba1f0401e5b
| author | iuc |
|---|---|
| date | Mon, 07 Oct 2024 06:45:22 +0000 |
| parents | c07ffa5e508d |
| children |
| rev | line source |
|---|---|
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2
c07ffa5e508d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 2bcb9bf1c90bee25a100f14f8ea28909aba89c9a
iuc
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changeset
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1 <tool id="samblaster" name="samblaster" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1"> |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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2 <description>marks duplicates, outputs split reads, discordant read pairs and unmapped reads</description> |
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2
c07ffa5e508d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 2bcb9bf1c90bee25a100f14f8ea28909aba89c9a
iuc
parents:
1
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changeset
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3 <macros> |
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3
595c942ad3ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 32feb54c292e406e2982f92284fb7ba1f0401e5b
iuc
parents:
2
diff
changeset
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4 <token name="@TOOL_VERSION@">0.1.26</token> |
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595c942ad3ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 32feb54c292e406e2982f92284fb7ba1f0401e5b
iuc
parents:
2
diff
changeset
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5 <token name="@VERSION_SUFFIX@">0</token> |
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2
c07ffa5e508d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 2bcb9bf1c90bee25a100f14f8ea28909aba89c9a
iuc
parents:
1
diff
changeset
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6 </macros> |
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1
de6d84a9bc8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
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7 <xrefs> |
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de6d84a9bc8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
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changeset
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8 <xref type="bio.tools">samblaster</xref> |
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de6d84a9bc8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
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changeset
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9 </xrefs> |
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0
cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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10 <requirements> |
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2
c07ffa5e508d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 2bcb9bf1c90bee25a100f14f8ea28909aba89c9a
iuc
parents:
1
diff
changeset
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11 <requirement type="package" version="@TOOL_VERSION@">samblaster</requirement> |
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3
595c942ad3ad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 32feb54c292e406e2982f92284fb7ba1f0401e5b
iuc
parents:
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diff
changeset
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12 <requirement type="package" version="1.0.1">sambamba</requirement> |
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0
cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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13 </requirements> |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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14 <version_command>samblaster --version</version_command> |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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15 <command detect_errors="exit_code"><![CDATA[ |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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16 #if $input.is_of_type('sam'): |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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17 #set stream="<(sambamba view -S -f bam -t ${GALAXY_SLOTS:-4} -h '%s')" % $input |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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18 #else: |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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19 #set stream="'%s'" % $input |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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20 #end if |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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21 sambamba view -t \${GALAXY_SLOTS:-4} -h <(sambamba sort -t \${GALAXY_SLOTS:-4} -n $stream -o /dev/stdout) | |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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22 samblaster |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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23 $output |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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24 $discordantFile |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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25 $splitterFile |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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26 $unmappedFile |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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27 $acceptDupMarks |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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28 $excludeDups |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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29 $removeDups |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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30 $addMateTags |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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31 $compatibility_mode |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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32 --maxSplitCount '$maxSplitCount' |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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33 --maxUnmappedBases '$maxUnmappedBases' |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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34 --minIndelSize '$minIndelSize' |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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35 --minNonOverlap '$minNonOverlap' |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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36 --minClipSize '$minClipSize' |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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37 #if $output != "-o /dev/null": |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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38 && sambamba sort -o output.bam -l 6 -t \${GALAXY_SLOTS:-4} <(sambamba view -S -f bam output.sam) |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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39 #end if |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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40 #if $discordantFile: |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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41 && sambamba sort -o discordant.bam -l 6 -t \${GALAXY_SLOTS:-4} <(sambamba view -S -f bam discordant.sam) |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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42 #end if |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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43 #if $splitterFile: |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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44 && sambamba sort -o splitter.bam -l 6 -t \${GALAXY_SLOTS:-4} <(sambamba view -S -f bam splitter.sam) |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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45 #end if |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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46 ]]></command> |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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47 <inputs> |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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48 <param argument="--input" type="data" format="bam,sam"/> |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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49 <param argument="--output" label="Output bam file for all input alignments" type="boolean" checked="true" truevalue="-o output.sam" falsevalue="-o /dev/null"/> |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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50 <param argument="--discordantFile" label="Output discordant read pairs?" type="boolean" truevalue="-d discordant.sam" falsevalue=""/> |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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51 <param argument="--splitterFile" label="Output split reads?" type="boolean" truevalue="-s splitter.sam" falsevalue=""/> |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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52 <param argument="--unmappedFile" label="Output unmapped/clipped reads as FASTQ?" type="boolean" truevalue="-u unmapped.fastq" falsevalue=""/> |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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53 <param argument="--acceptDupMarks" label="Accept duplicate marks already in input file instead of looking for duplicates in the input?" type="boolean" truevalue="-a" falsevalue=""/> |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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54 <param argument="--excludeDups" label="Exclude reads marked as duplicates from discordant, splitter, and/or unmapped file?" type="boolean" truevalue="-a" falsevalue=""/> |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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55 <param argument="--removeDups" label="Remove duplicates reads from all output files?" help="(Implies --excludeDups)" type="boolean" truevalue="-e" falsevalue=""/> |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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56 <param argument="--addMateTags" label="Add MC and MQ tags?" type="boolean" truevalue="--addMateTags" falsevalue=""/> |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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57 <param name="compatibility_mode" argument="-M" label="Run in compatibility mode?" help="Both 0x100 and 0x800 are considered chimeric. Similar to BWA MEM -M option." type="boolean" truevalue="-M" falsevalue="" /> |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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58 <param argument="--maxSplitCount" label="Maximum number of split alignments for a read to be included in splitter file." type="integer" value="2"/> |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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59 <param argument="--maxUnmappedBases" label="Maximum number of un-aligned bases between two alignments to be included in splitter file." type="integer" value="50" min="1"/> |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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60 <param argument="--minIndelSize" label="Minimum structural variant feature size for split alignments to be included in splitter file." type="integer" value="50" min="1"/> |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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61 <param argument="--minNonOverlap" label="Minimum non-overlaping base pairs between two alignments for a read to be included in splitter file." type="integer" value="20" min="1"/> |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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62 <param argument="--minClipSize" label="Minumum number of bases a mapped read must be clipped to be included in unmapped file." type="integer" value="20" min="1"/> |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
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63 </inputs> |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
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64 <outputs> |
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2
c07ffa5e508d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 2bcb9bf1c90bee25a100f14f8ea28909aba89c9a
iuc
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65 <data name="output_bam" format="bam" label="${tool.name} on ${on_string}: alignments" from_work_dir="output.bam"> |
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0
cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
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changeset
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66 <filter>output</filter> |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
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67 </data> |
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2
c07ffa5e508d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 2bcb9bf1c90bee25a100f14f8ea28909aba89c9a
iuc
parents:
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68 <data name="discordant_bam" format="bam" label="${tool.name} on ${on_string}discordant alignments" from_work_dir="discordant.bam"> |
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0
cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
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69 <filter>discordantFile</filter> |
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cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
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70 </data> |
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2
c07ffa5e508d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 2bcb9bf1c90bee25a100f14f8ea28909aba89c9a
iuc
parents:
1
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71 <data name="splitter_bam" format="bam" label="${tool.name} on ${on_string}: split alignments" from_work_dir="splitter.bam"> |
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0
cd001ec3c0c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 82097013a9eb5a6161d400e5b6c493113c440687
iuc
parents:
diff
changeset
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72 <filter>splitterFile</filter> |
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cd001ec3c0c6
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73 </data> |
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74 <data name="unmapped_fastq" format="fastqsanger" label="${tool.name} on ${on_string}: unmapped fastq" from_work_dir="unmapped.fastq"> |
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75 <filter>unmappedFile</filter> |
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76 </data> |
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77 </outputs> |
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78 <tests> |
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79 <test expect_num_outputs="3"> |
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80 <param name="input" value="sr.input.bam"/> |
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81 <param name="output" value="true"/> |
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82 <param name="discordantFile" value="false"/> |
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83 <param name="splitterFile" value="true"/> |
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84 <param name="unmappedFile" value="true"/> |
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85 <output name="output_bam" file="output.bam" compare="sim_size"/> |
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86 <output name="splitter_bam" file="splitters.bam" compare="sim_size"/> |
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87 <output name="unmapped_fastq"> |
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88 <assert_contents> |
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89 <has_line line="@M00860:26:000000000-A6UGV:1:1101:10000:6072" /> |
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90 </assert_contents> |
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91 </output> |
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92 </test> |
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93 <test expect_num_outputs="3"> |
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94 <param name="input" value="sr.input.sam.gz" ftype="sam"/> |
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95 <param name="output" value="true"/> |
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96 <param name="discordantFile" value="false"/> |
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97 <param name="splitterFile" value="true"/> |
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98 <param name="unmappedFile" value="true"/> |
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99 <output name="output_bam" file="output.bam" compare="sim_size"/> |
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100 <output name="splitter_bam" file="splitters.bam" compare="sim_size"/> |
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101 <output name="unmapped_fastq"> |
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102 <assert_contents> |
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103 <has_line line="@M00860:26:000000000-A6UGV:1:1101:10000:6072" /> |
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104 </assert_contents> |
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105 </output> |
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106 </test> |
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107 </tests> |
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108 <help><![CDATA[ |
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109 |
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110 *samblaster* |
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111 ============ |
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112 |
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113 Summary |
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114 ------- |
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115 |
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116 *samblaster* is a fast and flexible program for marking duplicates in |
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117 **read-id grouped** paired-end SAM files. It can also optionally output |
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118 discordant read pairs and/or split read mappings to separate SAM files, |
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119 and/or unmapped/clipped reads to a separate FASTQ file. When marking |
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120 duplicates, *samblaster* will require approximately 20MB of memory per |
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121 1M read pairs. |
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122 |
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123 Usage |
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124 ----- |
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125 |
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126 See the `SAM File Format |
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127 Specification <http://samtools.sourceforge.net/SAMv1.pdf>`__ for details |
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128 about the SAM alignment format. |
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129 |
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130 By default, samblaster marks duplicates with SAM FLAG 0x400. The |
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131 **--removeDups** option will instead remove duplicate alignments from the |
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132 output file. |
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133 |
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134 **ALIGNMENT TYPE DEFINITIONS:** Below, we will use the following |
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135 definitions for alignment types. Starting with *samblaster* release |
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136 0.1.22, these definitions are affected by the use of the **-M** option. |
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137 By default, *samblaster* will use the current definitions of alignment |
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138 types as specified in the `SAM |
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139 Specification <http://samtools.sourceforge.net/SAMv1.pdf>`__. Namely, |
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140 alignments marked with FLAG 0x100 are considered *secondary*, while |
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141 those marked with FLAG 0x800 are considered *supplemental*. If the |
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142 **-M** option is specified, alignments marked with either FLAG 0x100 or |
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143 0x800 are considered *supplemental*, and no alignments are considered |
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144 *secondary*. A *primary* alignment is always one that is neither |
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145 *secondary* nor *supplemental*. Only *primary* and *supplemental* |
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146 alignments are used to find chimeric (split-read) mappings. The **-M** |
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147 flag is used for backward compatibility with older SAM/BAM files in |
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148 which "chimeric" alignments were marked with FLAG 0x100, and should also |
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149 be used with output from more recent runs of *bwa mem* using its **-M** |
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150 option. |
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151 |
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152 **DISCORDANT READ PAIR IDENTIFICATION:** A **discordant** read pair is |
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153 one which meets all of the following criteria: |
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154 |
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155 1. Both side of the read pair are mapped (neither FLAG 0x4 or 0x8 is |
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156 set). |
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157 2. The *properly paired* FLAG (0x2) is not set. |
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158 3. *Secondary* or *supplemental* alignments are never output as |
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159 discordant, although a discordant read pair can have such alignments |
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160 associated with them. |
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161 4. Duplicate read pairs that meet the above criteria will be output as |
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162 discordant unless the **-e** option is used. |
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163 |
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164 **UNMAPPED/CLIPPED READ IDENTIFICATION:** An **unmapped** or **clipped** |
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165 read is a *primary* alignment that is unaligned over all or part of its |
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166 length respectively. The lack of a full alignment may be caused by a SV |
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167 breakpoint that falls within the read. Therefore, *samblaster* will |
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168 optionally output such reads to a FASTQ file for re-alignment by a tool, |
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169 such as `YAHA <https://github.com/GregoryFaust/yaha/>`__, geared toward |
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170 finding split-read mappings. *samblaster* applies the following strategy |
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171 to identify and output unmapped/clipped reads: |
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172 |
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173 1. An **unmapped** read has the *unmapped read* FLAG set (0x4). |
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174 2. A **clipped** read is a mapped read with a CIGAR string that begins |
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175 or ends with at least **--minClipSize** unaligned bases (CIGAR code S |
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176 and/or H), and is not from a read that has one or more *supplemental* |
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177 alignments. |
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178 3. In order for *samblaster* to output the entire sequence for clipped |
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179 reads, the input SAM file must have soft clipped primary alignments. |
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180 4. *samblaster* will output unmapped/clipped reads into a FASTQ file if |
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181 QUAL information is available in the input file, and a FASTA file if |
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182 not. |
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183 5. Unmapped/clipped reads that are part of a duplicate read pair will be |
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184 output unless the **-e** option is used. |
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185 |
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186 |
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187 **Written by:** Greg Faust (gf4ea@virginia.edu) `Ira Hall Lab, |
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188 University of Virginia <http://faculty.virginia.edu/irahall/>`__ |
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189 |
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190 **Please cite:** `Faust, G.G. and Hall, I.M., “\ *SAMBLASTER*: fast |
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191 duplicate marking and structural variant read extraction,” |
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192 *Bioinformatics* Sept. 2014; **30**\ (17): |
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193 2503-2505. <http://bioinformatics.oxfordjournals.org/content/30/17/2503>`__ |
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194 |
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195 **Also see:** `SAMBLASTER\_Supplemental.pdf |
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196 <https://github.com/GregoryFaust/samblaster/raw/master/SAMBLASTER_Supplemental.pdf>`__ |
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197 for additonal discussion and statistics about the duplicates marked by |
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198 *samblaster* vs. *Picard* using the NA12878 sample dataset. Click the |
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199 preceeding link or download the file from this repository. |
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200 **Written by:** Greg Faust (gf4ea@virginia.edu) `Ira Hall Lab, |
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201 University of Virginia <http://faculty.virginia.edu/irahall/>`__ |
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202 |
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203 **Please cite:** `Faust, G.G. and Hall, I.M., “\ *SAMBLASTER*: fast |
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204 duplicate marking and structural variant read extraction,” |
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205 *Bioinformatics* Sept. 2014; **30**\ (17): |
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206 2503-2505. <http://bioinformatics.oxfordjournals.org/content/30/17/2503>`__ |
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207 |
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208 **Also see:** `SAMBLASTER\_Supplemental.pdf |
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209 <https://github.com/GregoryFaust/samblaster/raw/master/SAMBLASTER_Supplemental.pdf>`__ |
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210 for additonal discussion and statistics about the duplicates marked by |
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211 *samblaster* vs. *Picard* using the NA12878 sample dataset. Click the |
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212 preceeding link or download the file from this repository. |
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213 |
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214 ]]></help> |
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215 <citations> |
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216 <citation type="doi">10.1093/bioinformatics/btu314</citation> |
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217 </citations> |
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218 </tool> |