Computes a fingerprint from the supplied input file (SAM/BAM or VCF) file and compares it to the expected fingerprint genotypes provided. The key output is a LOD score which represents the relative likelihood of the sequence data originating from the same sample as the genotypes vs. from a random sample. Two outputs are produced: (1) a summary metrics file that gives metrics at the single sample level (if the input was a VCF) or at the read level (lane or index within a lane) (if the input was a SAM/BAM) versus a set of known genotypes for the expected sample, and (2) a detail metrics file that contains an individual SNP/Haplotype comparison within a fingerprint comparison. The two files may be specified individually using the SUMMARY_OUTPUT and DETAIL_OUTPUT options. Alternatively the OUTPUT option may be used instead to give the base of the two output files, with the summary metrics having a file extension 'fingerprinting_summary_metrics' and the detail metrics having a file extension 'fingerprinting_detail_metrics'.
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