Mercurial > repos > john-mccallum > pcr_markers
comparison vcf_gff.xml @ 1:a0689dc29b7f draft
Updated vcf to gff conversion tool
| author | john-mccallum |
|---|---|
| date | Tue, 31 Jul 2012 00:33:11 -0400 |
| parents | |
| children | b321e0517be3 |
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| 0:21053f7f9ed1 | 1:a0689dc29b7f |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="vcf2gff_1" name="Convert vcf to gff"> | |
| 3 <description>Convert vcf to gff</description> | |
| 4 <command interpreter="python">vcf_gff.py $inputVcf $outputfile</command> | |
| 5 <inputs> | |
| 6 <param format="vcf" name="inputVcf" type="data" label="vcf file containing SNP data"/> | |
| 7 </inputs> | |
| 8 <outputs> | |
| 9 <data format="gff3" name="outputfile" /> | |
| 10 </outputs> | |
| 11 <help> | |
| 12 | |
| 13 ** Convert vcf to gff3** | |
| 14 | |
| 15 This tool takes vcf output from Samtools mpileup and converts to gff3 format. | |
| 16 It converts a single vcf output file containing output from a single bam file or from multiple bam files. | |
| 17 Read counts and GT scores are used as an indicator of whether a mutation is homozygous or heterozygous and outputs in the INFO section. | |
| 18 | |
| 19 **TIP** | |
| 20 mpileup **must** be run with Genotype Likelihood Computation selected (-g flag)to generate the GT flag in BCF/VCF output. | |
| 21 This then used to estimate the SNP presence in one or more samples. | |
| 22 More info is available in the manual pages at: http://samtools.sourceforge.net/mpileup.shtml | |
| 23 | |
| 24 | |
| 25 **Example** | |
| 26 | |
| 27 --input vcf | |
| 28 | |
| 29 :: | |
| 30 | |
| 31 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bam | |
| 32 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 | |
| 33 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 | |
| 34 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 | |
| 35 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 | |
| 36 | |
| 37 --output gff | |
| 38 | |
| 39 :: | |
| 40 | |
| 41 #CHROM SOURCE TYPE START STOP QUAL STRAND PHASE INFO | |
| 42 PGSC0003DMB000000001 SAMTOOLS SNP 430 430 3.41 . . ID=PGSC0003DMB000000001:SNP:430;Variant_seq=T;Reference_seq=A;Total_reads=4:Zygosity=2:HOM_mut | |
| 43 PGSC0003DMB000000001 SAMTOOLS SNP 445 445 3.41 . . ID=PGSC0003DMB000000001:SNP:445;Variant_seq=T;Reference_seq=G;Total_reads=4:Zygosity=2:HOM_mut | |
| 44 PGSC0003DMB000000001 SAMTOOLS SNP 446 446 3.41 . . ID=PGSC0003DMB000000001:SNP:446;Variant_seq=A;Reference_seq=G;Total_reads=4:Zygosity=2:HOM_mut | |
| 45 PGSC0003DMB000000001 SAMTOOLS SNP 452 452 3.41 . . ID=PGSC0003DMB000000001:SNP:452;Variant_seq=T;Reference_seq=C;Total_reads=4:Zygosity=2:HOM_mut | |
| 46 | |
| 47 | |
| 48 | |
| 49 ----------------------- | |
| 50 | |
| 51 *If you use this tool please cite:* | |
| 52 | |
| 53 A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data: | |
| 54 Application For Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.) | |
| 55 (2012) | |
| 56 | |
| 57 Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright, | |
| 58 Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum | |
| 59 | |
| 60 </help> | |
| 61 </tool> |