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author iuc
date Thu, 30 May 2019 21:14:37 -0400
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children 16eccd223c6e
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1 <tool id="basil" name="basil" version="1.2.0">
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2 <description>Breakpoint detection, including large insertions</description>
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3 <requirements>
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4 <requirement type="package" version="1.2.0">anise_basil</requirement>
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5 </requirements>
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6 <version_command>basil --version 2>&amp;1 | grep 'basil version' | cut -f 3 -d ' '</version_command>
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7 <command detect_errors="aggressive"><![CDATA[
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8 ln -s '$ref' 'ref.fa' &&
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9 ln -s '$bam' 'in.bam' &&
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10 ln -s '$vcf' 'out.vcf' &&
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11 basil
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12 --input-reference 'ref.fa'
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13 --input-mapping 'in.bam'
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14 --out-vcf 'out.vcf'
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15 --oea-min-support-each-side '$min_oea_each_side'
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16 ]]></command>
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17 <inputs>
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18 <param name="ref" argument="--input-reference" type="data" format="Fasta" label="Reference Sequence File" help="FASTA file with the reference."/>
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19 <param name="bam" argument="--input-mapping" type="data" format="sam,bam" label="Alignment File" help="SAM/BAM file to use as the input."/>
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20 <param name="min_oea_each_side" argument="--oea-min-support-each-side" type="integer" value="2" label="Minimum supporting reads, each side" help="Smallest number of OEA (one-end-anchor) reads on each side to support an insertion. In range [1..inf]. This is the minimum number of supporting reads (without mapped partners) on each side of an insertion breakpoint required to not be filtered." />
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21 </inputs>
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22 <outputs>
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23 <data name="vcf" format="vcf" />
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="ref" value="ref.fa"/>
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28 <param name="bam" value="simulated.bam"/>
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29 <param name="min_oea_each_side" value="2"/>
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30 <output name="vcf" file="basil.vcf"/>
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31 </test>
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32 </tests>
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33 <help><![CDATA[
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34 BASIL is a method to detect breakpoints for structural variants (including insertion breakpoints) from aligned paired HTS reads in BAM format. Use BASIL to analyze BAM files for tentative insertion sites.
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35
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36 Note that BASIL will in general detect all kinds of breakpoints, e.g. for inversions on real-world data.
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37
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38 BASIL VCF fields
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39
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40 A typical line in BASIL might look as follows.
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41
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42 1 5001 site_0 T <INS> . PASS IMPRECISE;SVTYPE=INS GSCORE:CLEFT:CRIGHT:OEALEFT:OEARIGHT 46.4256:10:12:35:32
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43
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44 The first seven columns are as usually in VCF files (ref name, 1-based position, reference base, abbreviation for long insertion, no assigned quality, passing all filters, imprecise insertion SV).
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45
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46 The eighth column contains the names of the score values given in the ninth column:
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47
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48 GSCORE Geometric mean of the sum of "1 + $score" for all of the following scores.
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49 CLEFT Number of clipping signatures supporting the site from the left side.
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50 CRIGHT Number of clipping signatures supporting the site from the right side.
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51 OEALEFT Number of OEA alignments supporting the site from the left.
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52 OEARIGHT Number of OEA alignmetns supproting the site from the right.
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53
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54 Generally, one should filter for a minimum support of OEA records on each side, e.g. a value of 10 makes sense for a 30x coverage and showed good results on simulated data.
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55
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56 For a ranking, GSCORE is a suitable measure but we did not develop any statistical model for BASIL matches and it is a mean of pseudocounts only. It carries no statistically precise meaning.
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57 ]]></help>
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58 <citations>
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59 <citation type="doi">10.1093/bioinformatics/btv051</citation>
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60 </citations>
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61 </tool>