This repository is a collection of miscellaneous scripts that perform various small tasks.
| Script | Quick Description |
|---|---|
bed_file_summary.R |
Provides mean, five number summary and total length of capture region size of a BED file. |
coverage_summary.sh |
Generates Min, Q1, Median, Mean, Q3, and Max coverage summaries using bedtools given a list of BAM files and a BED file. |
get_reverse_complement |
Directory that contains scripts and documentation to get the reverse complement of sequences. |
HarvEST_subset_by_chr.sh |
Takes a HarvEST SNP_BAC.txt file that has PhysPos and Chr_2016 (see SNP_PhysPosition_Matching.R script for merging by PhysPos) columns and subsets the data by chromosome. The script returns a new file for every subset group. |
HarvEST_to_BED.R |
Takes a HarvEST file that has PhysPos and Chr_2016 (see SNP_PhysPosition_Matching.R script for merging by PhysPos) info based on the new barley reference genome and creates a BED file with 4th column containing SNP ID. The output file was intented to be passed to bedops. |
LD_data_prep.sh |
Prior to running LDheatmap.R, run this script to: 1) Generate sample list containing snps of interest. 2) Make sure genotyping data and sample lists are sorted correctly and duplicates are filtered out. |
LDheatmap.R |
This script generates LD heatmaps using genotyping data and physical position information. Please run LD_data_prep.sh prior to running this script. |
makeGenotypes.R |
This script converts columns in genotype data frame to a format accepted by R package, LDheatmap. |
random_sampler.R |
Randomly samples names/values from a given list |
renaming_files |
This directory contains file renaming scripts. See readme in the directory for more details. |
SNP_PhysPosition_Matching.R |
Takes VCF file (containing physical position, SNP ID, and Chr info) and HarvEST file and adds Physical Position and Chr_2016 columns based on matching SNP names. Note: this script discards any SNPs that do not have matching SNP names. |
snpBAC_NA_filtering.R |
Removes all rows with empty cells in Query_SNP column and missing info for PhysPos column. |
transpose_data.R |
Transposes data frames |