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

SNP densities

Description

Calculate SNP densities along chromosome from a VCF file

Dependencies

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

Input file

VCF file: File with SNPs

Parameters

Step: Step in bp for the window to calculate SNP density
Output name: Output base name for the two ouput files

Output files

Output_name: Tabular file with SNP density in each postion
Output_name.by_sample: Tabular file with SNP density for each sample

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  CATB1
chr1    2209    .       G       T       213.84  .       AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=0;QD=30.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|)    GT:AD:DP:GQ:PL  1/1:0,7:7:18:242,18,0

Parameters

Step -> 200000

Output name -> densities

Output files

densities

Chromosome Position SNPs
chr1       200000   355
chr1       400000   228
chr1       600000   63
chr1       800000   191

densities.by_sample

Chromosome BA58 BA59 BD54
chr1       220  197  225
chr1       130  119  133
chr1       43   43   40
chr1       139  167  141