The conform-gt program first finds pairs of Supporting minor allele frequency or correlation evidence. If strict=true strand determination requires Minor allele frequency or correlation evidence will be used Will be performed using only allele labels if that is possible, and Strict= true or false specifies the algorithm used to determine whether a referenceĪnd target VCF record reflect the same chromosome strand With ancestry from more than continent, you should use theĮxcludesamples parameter to limit statisticalĪnalysis to samples from a one continental population. If the reference or target data contains samples (one sample identifier per line) when using allele frequencyĪnd correlation evidence to determine whether a referenceĪnd target VCF record reflect the same chromosome strand. If the reference and target VCF files use different genomeĬoordinates (NCBI builds), you must use match=ID.Įxcludesamples= file specifies a file containing samples to be excluded The POS field will be used (default: match=ID). Optional Parameters match= ID or POS specifies the field used to match reference out= prefix specifies the prefix for output filenames. Outside the chromosome or chromosome interval will be ignored. Must be identical in target and reference files. chrom= chrom or chrom= chrom:start-end specifies a chromosome or chromosome interval:Įnd is an end position. gt= file specifies the VCF file with target genotype (GT) data. Required Parameters ref= file specifies the VCF file with reference genotype (GT) data. Parameters, each expressed as parameter=value. Where arguments is a space-separated list of To use conform-gt, enter the following command VCF records are permitted to have multiple non-reference alleles. Adjust target VCF records so that chromosome strandĪnd allele order match the VCF reference file.To determine chromosome strand in ambiguous cases. Makes use of allele frequency and inter-marker correlation Exclude target VCF records whose chromosome strandĬannot be determined.Exclude target VCF records which cannot be matched to any.Find corresponding VCF records in the target and reference files.The reference and target VCF files are each required to haveĭata for at least 20 individuals so that the statistical tests
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