(relatively) Simple to use commandline tools for the manipulation and analysis of VCF files, geared towards the identification of pathogenic mutations in Mendelian disease.
- filter SNPs on minor allele frequency and/or SNP build
- filter on EVS minor allele frequency
- filter on allele frequency in other VCFs
- filter on samples
- find biallelic (compound het or homozygous) variants in one or more samples/families
- find de novo variants
- annotate gene information to VEP output
- write output summary to .xlsx spreadsheet
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