miscellaneous_scripts

A collection of random scripts for a variety of purposes. These have been put together on the fly and are likely bad scripts, please don't judge me too harshly.

count_liftover_fail.awk

• Script for counting reasons why variants failed liftover with CrossMap.
• USAGE: awk -f count_liftover_fail.awk /path/to/crossMap_output.vcf.unmap

splice_AI_filt.sh

• Script for filtering VCF files output from SpliceAI and returning inforamtion about variants that have score above specified threshold.
• bash splice_AI_filt.sh /path/to/spliceAI_output.vcf.gz minimum_score_threshold > splice_vars_output.txt

linkage_subset_vcf.sh

• Scfipt to select individuals from multisample vcf and filter down to only variants withing a specified interval
• USAGE: bash linkage_subset_vcf.sh /path/to/file_containing_variants.vcf.gz comma,separated,sample,list output_prefix chr:start-end

whole_genome_linkage_plots.R

• Script containing functions to generate whole genome linkage plots with R using the output "-parametric.tbl" files produced by Merlin.
• This script cotains a function to generate these plots for a single interation of linkage analysis (plot_genome_linkage) and one to take in multiple iterations of a linkage analysis, sum together the LOD scores, and plot summed totals (plot_combined_genome_linkage).