Detect Copy Number Variants from SNPs Data
Correct allele depth values
Generate allele frequency table for individuals or populations
Get allele information for duplicate detection
Find CNVs from deviants
Calculate normalized depth for alleles
Simulate median allele ratios for varying number of samples and depth ...
Plot classified SNPs into deviants/CNVs and non-deviants/non-CNVs
Validate detected deviants/cnvs
Detect deviants from SNPs; classify SNPs
Export VCF files
Get missingness of individuals in raw vcf
Format genotype for BayEnv and BayPass
Determine per sample heterozygosity and inbreeding coefficient
Generate allele depth or genotype table
Remove MAF allele
Calculate normalization factor for each sample
Simulate and plot detection power of bias in allele ratios
Import VCF file
Determine pairwise relatedness
Identify significantly different heterozygotes from SNPs data
Simulate Allele Frequencies
Get sequencing quality statistics of raw VCF files (with GatK generate...
Calculate population-wise Vst
Run permutation on Vst
Functions in this package will import filtered variant call format (VCF) files of SNPs data and generate data sets to detect copy number variants, visualize them and do downstream analyses with copy number variants(e.g. Environmental association analyses).
Useful links