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1 <?xml version="1.0"?>
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2 <tool id="vcf2gff_1" name="Convert vcf to gff">
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3 <description>Convert vcf to gff</description>
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4 <command interpreter="python">vcf_gff.py $inputVcf $outputfile</command>
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5 <inputs>
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6 <param format="vcf" name="inputVcf" type="data" label="vcf file containing SNP data"/>
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7 </inputs>
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8 <outputs>
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9 <data format="gff3" name="outputfile" />
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10 </outputs>
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5
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11 <tests>
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12 <test>
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13 <param name="inputVcf" value="mpileup_out.vcf" ftype="vcf"/>
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14 <output name="outputfile" file="mpileup_vcf_to_gff_output.gff"/>
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15 </test>
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16 <test>
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17 <param name="inputVcf" value="freebayes_out.vcf" ftype="vcf"/>
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18 <output name="outputfile" file="freebayes_vcf_to_gff_output.gff"/>
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19 </test>
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20 </tests>
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1
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21 <help>
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22
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23 ** Convert vcf to gff3**
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24
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25 This tool takes vcf output from Samtools mpileup and converts to gff3 format.
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26 It converts a single vcf output file containing output from a single bam file or from multiple bam files.
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27 Read counts and GT scores are used as an indicator of whether a mutation is homozygous or heterozygous and outputs in the INFO section.
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28
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29 **TIP**
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30 mpileup **must** be run with Genotype Likelihood Computation selected (-g flag)to generate the GT flag in BCF/VCF output.
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31 This then used to estimate the SNP presence in one or more samples.
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32 More info is available in the manual pages at: http://samtools.sourceforge.net/mpileup.shtml
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33
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34
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35 **Example**
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36
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37 --input vcf
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38
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39 ::
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40
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41 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bam
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42 PGSC0003DMB000000001 430 . A T 3.41 . DP=4;AF1=0.9904;CI95=0.125,1;DP4=0,0,2,0;MQ=17 PL:DP:GT:GQ 32,6,0:2:1/1:23
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43 PGSC0003DMB000000001 445 . G T 3.41 . DP=4;AF1=0.9904;CI95=0.125,1;DP4=0,0,2,0;MQ=17 PL:DP:GT:GQ 32,6,0:2:1/1:23
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44 PGSC0003DMB000000001 446 . G A 3.41 . DP=4;AF1=0.9904;CI95=0.125,1;DP4=0,0,2,0;MQ=17 PL:DP:GT:GQ 32,6,0:2:1/1:23
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45 PGSC0003DMB000000001 452 . C T 3.41 . DP=4;AF1=0.9904;CI95=0.125,1;DP4=0,0,2,0;MQ=17 PL:DP:GT:GQ 32,6,0:2:1/1:23
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46
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47 --output gff
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48
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49 ::
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50
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51 #CHROM SOURCE TYPE START STOP QUAL STRAND PHASE INFO
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52 PGSC0003DMB000000001 SAMTOOLS SNP 430 430 3.41 . . ID=PGSC0003DMB000000001:SNP:430;Variant_seq=T;Reference_seq=A;Total_reads=4:Zygosity=2:HOM_mut
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53 PGSC0003DMB000000001 SAMTOOLS SNP 445 445 3.41 . . ID=PGSC0003DMB000000001:SNP:445;Variant_seq=T;Reference_seq=G;Total_reads=4:Zygosity=2:HOM_mut
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54 PGSC0003DMB000000001 SAMTOOLS SNP 446 446 3.41 . . ID=PGSC0003DMB000000001:SNP:446;Variant_seq=A;Reference_seq=G;Total_reads=4:Zygosity=2:HOM_mut
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55 PGSC0003DMB000000001 SAMTOOLS SNP 452 452 3.41 . . ID=PGSC0003DMB000000001:SNP:452;Variant_seq=T;Reference_seq=C;Total_reads=4:Zygosity=2:HOM_mut
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56
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57
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58
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59 -----------------------
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60
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61 *If you use this tool please cite:*
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62
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63 A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data:
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64 Application For Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.)
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65 (2012)
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66
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67 Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright,
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68 Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum
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69
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70 </help>
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71 </tool>
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