Convert vcf file to table format with script: 'vcf_to_genotypeTab_meta.Rscript'
- usage example: ./vcf_to_genotypeTab_meta.Rscript -i=testSNPs.vcf
- input: vcf file (e.g. GATK vcf file) - optional arguments: '-acgt' : include this flag to output nucleotide genotypes (default: on) '-meta' : include this flag to output metadata tables (default: on)
- output: tab-delimited table with genotypes AND tab-delimited tables with genotype metadata: AD: allele depth DP: read depth GQ: genotype quality PL: phred likelihood
- the genotypes dataframe can be used in downstream analyses
- this script is meant to be run as an executable Rscript
- genotype format: 0 represents homozygous reference allele 1 represents heterozygous 2 represents homozygous alternative allele NA represents missing data
PCA plot with script: 'snps_PCA.Rscript'
- purpose - Make Principal Components Analysis (PCA) plot from SNP genotypes
- usage example: ./snps_PCA.Rscript -i=testSNPs.GT.tab OR ./snps_PCA.Rscript testSNPs.GT.tab
- input: GT table where genotypes are coded 0,1,2, ...
- output: PCA plot