Merge branch 'master' of https://github.com/rbutleriii/Clinotator

README.md

@@ -48,6 +48,10 @@ Three required bits of information: **(1)** the type of input file, **(2)** the
 
 Additional arguments include a log file (--log), a more detailed log file (--long-log) and specification of the output file prefix (-o, the default is clinotator). Also help and version messages are available.
 
+### A Note on Input Type
+
+The preferred input file types are a VID list or a vcf file. The rsID list alone is inherently ambiguous, as multi-allelic rsIDs can have several VIDs associated, and vice versa. The rsID to VID conversion is not 1:1, so the table file generated will return rows for all possible VIDs associated with the rsID, and one row for each alternate allele. The rsID generated table may thus require additional matching using the alternate allele column (CVAL). Vcf files will only be annotated with the correct rsID/alternate allele combination. The ‘vcf_match’ field addresses the reverse situation (multiple rsIDs in a single VID), by identifying all rsIDs associated with a VID and its haplotype status.
+
 ## Motivation
 
 While ClinVar has become an indispensable resource for clinical variant interpretation, its sophisticated structure provides a daunting learning curve. Often the sheer depth of types of information provided can make it difficult to analyze variant information with high throughput. Clinotator is a fast and lightweight tool to extract important aspects of criteria-based clinical assertions and uses that information to generate several metrics to assess the strength and consistency of the evidence supporting the variant clinical significance. Clinical assertions are weighted by significance type, age of submission and submitter expertise category to filter outdated or incomplete assertions that otherwise confound interpretation. This can be accomplished in batches: either lists of Variation IDs or dbSNP rsIDs, or with vcf files which are additionally annotated. Clinotator slices out problem variants in minutes without extensive computational effort—just using a personal computer. With the rapidly growing body of variant evidence, most submitters and researchers have limited resources to devote to variant curation. Clinotator provides efficient, systematic prioritization of discordant variants in need of reclassification. The hope is that this tool can inform ClinVar curation and encourage submitters to keep their clinical assertions current by focusing their efforts. Additionally, researchers can utilize new metrics to analyze variants of interest in pursuit of new insights into pathogenicity.