Releases: solelena/PSReliP
Releases · solelena/PSReliP
PSReliP 1.1.1 The release with the changes made for the variants ID.
In previous releases, a combination of the chromosome name and the position at which the variant is located was used as the variant identifier. In this release, we kept it in case the variant ID is not in the VCF/BCF file. If the variant ID is listed in the VCF/BCF file, we saved it for further analysis. To do this, changes were made to the ps_pl2_pvar_edit.pl program, which is executed in the first script (pre_analysis_first_script.sh).
PSReliP 1.1 Release with the addition of a filter on the number of samples that are plotted on the heatmaps.
- A filter by the number of samples has been added to the analysis_second_script.sh file to decide whether heatmaps of the IBS, GRM and kinship matrices will be built. If the number of samples is ≤ 400, heatmaps will be plotted.
- Two app.R files have been added for the case where the number of samples is > 400 and no heatmap is generated.
- At the end of the PSReliP analysis stage, the second shell script (analysis_second_script.sh) compresses the resulting Shiny application directory into a single zip file with the same name as this directory.
First version of PSReliP
This is the first version of PSReliP
Features
- QC and and filtering of samples and variants;
- calculation of basic sample statistics, such as the types of observed variants, inbreeding coefficients, etc., and performing the before and after data filtering;
- analysis of PS using PCA and MDS, and complete-linkage hierarchical clustering of samples based on the IBS distance matrix, if selected;
- calculation of Wright's FST;
- calculation of the IBS distance matrix and analysis of genetic relatedness by estimating the KING kinship coefficient matrix and GRM;
- interactive visualization of the analysis results using Shiny technology;
- ability for users to download analysis results and all plotted graphs using the web interface.