snpSniffer

-- About snpSniffer --

snpSniffer is a genotype based sample integrity checking tool for next generation sequencing data. It ensures no sample mixups have occurred by checking genotype concordance of carefully curated genomic loci. It currently works on whole genome, exome and RNA-Seq data.

Identifying mixups involves 3 steps
1. Generate the genotypes in a vcf format at specific genomic loci
2. Adding the genotypes generated to a flat file "database.ini" provided
3. Compare the genotypes for samples of interest, examine the snpSniffer output and infer if any mixups occurred

All the above steps can be run using snpSniffer