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-I file containing list of intervals []
-I file containing list of intervals []
-i intervals
-i intervals
-? displays help
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=== Estimate ===
Compute features in a VCF file. Example of statistics are Allele counts, [[Genotype_Likelihood_based_Inbreeding_Coefficient|Genotype Likelihood based Inbreeding Coefficient]].
[[Genotype_Likelihood_based_Allele_Frequency|Hardy-Weinberg Genotype Likelihood based Allele Frequencies]]
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#compute features for the variants found in vt.vcf
#requires GT, PL and DP
vt compute_features vt.vcf
#annotates variants with the following fields
##INFO=<ID=AC,Number=A,Type=Integer,Description="Alternate Allele Counts">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total Number Allele Counts">
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=AF,Number=A,Type=Float,Description="Alternate Allele Frequency">
##INFO=<ID=GC,Number=G,Type=Integer,Description="Genotype Counts">
##INFO=<ID=GN,Number=1,Type=Integer,Description="Total Number of Genotypes Counts">
##INFO=<ID=GF,Number=G,Type=Float,Description="Genotype Frequency">
##INFO=<ID=HWEAF,Number=A,Type=Float,Description="Genotype likelihood based MLE Allele Frequency assuming HWE">
##INFO=<ID=HWEGF,Number=G,Type=Float,Description="Genotype likelihood based MLE Genotype Frequency assuming HWE">
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Genotype likelihood based MLE Allele Frequency">
##INFO=<ID=MLEGF,Number=G,Type=Float,Description="Genotype likelihood based MLE Genotype Frequency">
##INFO=<ID=HWE_LLR,Number=1,Type=Float,Description="Genotype likelihood based Hardy Weinberg ln(Likelihood Ratio)">
##INFO=<ID=HWE_LPVAL,Number=1,Type=Float,Description="Genotype likelihood based Hardy Weinberg Likelihood Ratio Test Statistic ln(p-value)">
##INFO=<ID=HWE_DF,Number=1,Type=Integer,Description="Degrees of freedom for Genotype likelihood based Hardy Weinberg Likelihood Ratio Test Statistic">
##INFO=<ID=FIC,Number=1,Type=Float,Description="Genotype likelihood based Inbreeding Coefficient">
##INFO=<ID=AB,Number=1,Type=Float,Description="Genotype likelihood based Allele Balance">
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usage : vt compute_features for variants [options] <in.vcf>
options : -s print site information only without genotypes [false]
-o output VCF/VCF.GZ/BCF file [-]
-f filter expression []
-I File containing list of intervals
-i Intervals
-? displays help
-? displays help
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