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vcf_gff.xml
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vcf_gff.xml
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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>