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 annotation statistics

Description

Get annotation statistics from VCF

Dependencies

VCFtools: vcftools 0.1.14, Conda version
Bioperl: perl-bioperl 1.6.924, Conda version

Input file

VCF file: VCF file

Parameters

Step: Step in bp
Output label: Prefix for the ouput files

Output files

Output_name

Output_name.effect file

Output_name.location file

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

Parameters

Step -> 50000 Output label -> VCF_stats

Output files

VCF_stats

Chrom   Bin     dN/dS ratio
chr1    50000   0.791666666666667
chr1    100000  0.981132075471698
chr1    150000  2.08333333333333

VCF_stats.effect

Intron  960     Intron:960
UTR     281     UTR:281
Exon    3248    Synonym:124     Non-syn:120

VCF_stats.location

Intergenic      466     Intergenic:466
Genic   4489    Exon:3248       Intron:960      UTR:281