gt_omics_analysis_toolkit

A growing collection of custom executables for bioinformatics analysis

Filter VCF:

Filtering a VCF file by include biallelic SNPs only, with minimum genotype quality, sample and snp missingness with optional sample_list filter specified by user.

Usage: bash shell_scripts/filter_vcf.sh <filename.vcf.gz> <max SNP missingness> <max sample missingness> <genotype quality> <output directory> <sample prefix> [sample list.txt]"

Plot SNP and Sample Missingness:

First, make missingness tables. Run:

bash filter_vcf.sh <filename.vcf.gz> <max SNP missingness> <max sample missingness> <genotype quality> <output directory> <sample prefix> [sample list.txt]"

Then plot the sample and snp missingness histograms. Run:

module load r

Rscript Rscripts/plot_site_and_sample_missingness.R prefix <sample_prefix> <output_path> <sample_missingness_histogram_data.tsv> <snp_missingness_histogram_data.tsv>

R Shiny app for dynamically filtering VCF and plotting missingness (In Progress)