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<?xml version="1.0"?>
<tool id="vcf2gff_1" name="Convert vcf to gff">
  <description>Convert vcf to gff</description>
  <command interpreter="python">vcf_gff.py $inputVcf  $outputfile</command>
  <inputs>
    <param format="vcf" name="inputVcf" type="data" label="vcf file containing SNP data"/>
  </inputs>
  <outputs>
     <data format="gff3" name="outputfile" />
  </outputs>
  <tests>
        <test>
                <param name="inputVcf" value="mpileup_out.vcf" ftype="vcf"/>
                <output name="outputfile" file="mpileup_vcf_to_gff_output.gff"/>
        </test>
        <test>
                <param name="inputVcf" value="freebayes_out.vcf" ftype="vcf"/>
                <output name="outputfile" file="freebayes_vcf_to_gff_output.gff"/>
        </test>
  </tests>
<help>

** Convert vcf to gff3**

This tool takes vcf output from Samtools mpileup and converts to gff3 format.
It converts a single vcf output file containing output from a single bam file or from multiple bam files.
Read counts and GT scores are used as an indicator of whether a mutation is homozygous or heterozygous and outputs in the INFO section.

**TIP**
mpileup **must** be run with Genotype Likelihood Computation selected (-g flag)to generate the GT flag in BCF/VCF output. 
This then used to estimate the SNP presence in one or more samples.  
More info is available in the manual pages at: http://samtools.sourceforge.net/mpileup.shtml


**Example**

--input vcf

::

	#CHROM    POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  bam
	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
	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 
	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 
	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

--output gff

::

	#CHROM    SOURCE    TYPE    START    STOP    QUAL    STRAND   PHASE    INFO
	PGSC0003DMB000000001    SAMTOOLS        SNP     430     430     3.41    .       .       ID=PGSC0003DMB000000001:SNP:430;Variant_seq=T;Reference_seq=A;Total_reads=4:Zygosity=2:HOM_mut
	PGSC0003DMB000000001    SAMTOOLS        SNP     445     445     3.41    .       .       ID=PGSC0003DMB000000001:SNP:445;Variant_seq=T;Reference_seq=G;Total_reads=4:Zygosity=2:HOM_mut
	PGSC0003DMB000000001    SAMTOOLS        SNP     446     446     3.41    .       .       ID=PGSC0003DMB000000001:SNP:446;Variant_seq=A;Reference_seq=G;Total_reads=4:Zygosity=2:HOM_mut
	PGSC0003DMB000000001    SAMTOOLS        SNP     452     452     3.41    .       .       ID=PGSC0003DMB000000001:SNP:452;Variant_seq=T;Reference_seq=C;Total_reads=4:Zygosity=2:HOM_mut



-----------------------

*If you use this tool please cite:*

A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data: 
Application For  Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.)
(2012)

Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright, 
Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum

</help>
</tool>