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Get Haplotypes From Phased VCF (version 2.0.0)

Authors Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform

Please cite "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", Dereeper A. et al., Nucl. Acids Res. (1 july 2015) 43 (W1).

Galaxy integration Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA)

Support For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr

Get Haplotypes From Phased VCF

Description

Get Haplotype from phased VCF

Input file

VCF file: Phased VCF file

Parameter

Output file basename: Prefix for the output VCF file

Output files

Distinct Haplotypes text file: File describing distincts haplotypes
Fasta file: Fasta file with haplotypes
Distinct Haplotypes fasta file: Fasta file with distincts haplotypes

Working example

Input file

VCF file

#fileformat=VCFv4.1
#FILTER=&lt;ID=LowQual,Description="Low quality">
#FORMAT=&lt;ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
[...]
CHROM   POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  AZUCENA
Chr1    4299    .       G       A       .       PASS    AR2=1;DR2=1;AF=0.168    GT:DS:GP        0|0:0:1,0,0

Parameter

Output name -> haplotypes

Output files

haplotypes.distinct_haplotypes.txt

===Chr10===
haplo1:2:CIRAD403_1,CIRAD403_2,
TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACAT
haplo2:2:MAHAE_1,MAHAE_2,
TAAATCTTGGTGCTGATCTGATATTTAATGCGT

haplotypes.haplo.fas

>Chr10_AZUCENA_1
TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACAT
>Chr10_AZUCENA_2
TAAATCTTGGTGCTGATCTGATATTTAATGCGT

haplotypes.distinct_haplotypes.fas

>haplo1|2
CAATTTATATATACTTGTATATAACCACAACGAGAGAGTTTTACCT
TTTATAAAAAATAAATAATGTATTACGGCTAATATAGCAATCTTTT
AAAATAAATCTATATTTAAATGACTATGGAATTACTAATCACAATA
ACAGGATCTTGTTATTTTTAGCTTGTGTACTTATAATGATCCGATG
>haplo2|2
GCTACTTAAATATCTAGCATTAATCCACAACGAGAGGCTCTTACCT
TTAAAAAAGGGTCATCGCCTATAGGTTAGATAATCGACACATATAA
TTATAAGAAATTATATATAATTTTTAATCTAGTTCATTCTTGTGCA
TCATTATGTTATATAATAATAAACGTAACAAATATTGATACTACTC