Man pages for IDEELResearch/vcfR2manip
Basic functions for manipulating VCFs within the VCFR object/R environment
| binomial_draw_gtmat012_imputation | Perform GT Imputation, Loci-by-Loci for Biallelic |
| bivcfR2segsites_wsaf | bivcfR2segsites_wsaf |
| calc_loci_missingness_by_smpl | Filter VCF based on given loci missingness by sample |
| corMat | cormat |
| EB_for_wsaf | Perform Empirical Bayes Shrinkage, Loci-by-Loci |
| genautocorr | genautocorr setup |
| GFF2VariantAnnotation_Short | gff2geneannotation |
| gtmat012 | vcfR2removesingletons_gt |
| NRAFdf2Fw_pairwisegendist | NRAFlist2Fw_pairwisegendist |
| plot_vcfRobj_GT | Plot vcfR Object GT Matrix |
| select_samples | Select Samples from VCF |
| vcffilter_ChromPos | vcffilter_ChromPos |
| vcffilter_format | vcfR2vcffilter_FORMAT |
| vcffilter_info | vcfR2vcffilter_INFO |
| vcf_loci_splitter | Split a VCF to Individual Loci |
| vcfR2Fw_pairwisegendist | vcfR2Fw_pairwisegendist |
| vcfR2LDfiltered | vcfR2LDfiltered |
| vcfR2nohetsmonoclonal_gt | Remove heterozygote calls and make monoclonal |
| vcfR2removepoorcovloci_dp | vcfR2removepoorcovloci_dp |
| vcfR2removesingletons_gt | vcfR2removesingletons_gt |
| vcfR2segsites_gt | vcfR2segsites_gt |
| vcfR2SubsetChrom | vcfR2SubsetChrom |
| vcfR2SubsetChromPos | vcfR2SubsetChromPos |
| vcfR2thap | rehh liftover for vcfR |
| wicalc | DAB weight calculator |
