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=== Compute Features ===

=== Estimate ===

Compute features in a VCF file.  Example of statistics are Allele counts, [[Genotype_Likelihood_based_Inbreeding_Coefficient|Genotype Likelihood based Inbreeding Coefficient]].

  Compute variant based estimates.  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]]

  [[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

   #compute features for the variants found in vt.vcf

   #requires GT, PL and DP

   #requires GT and PL

   vt compute_features vt.vcf

   vt estimate -e AF,MLEAF vt.vcf

  ##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">

              AC       : Alternate Allele counts

              AN       : Total allele counts

              NS       : No. of samples.

  ##INFO=<ID=GF,Number=G,Type=Float,Description="Genotype Frequency">

              AF       : Alternate allele frequencies.

  ##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">

              MLEGF    : Genotype frequencies.

  HWEAF     GL based allele frequencies estimates assuming HWE

   ##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)">

              HWEGF     : Genotype frequencies derived from HWEAF.

  ##INFO=<ID=HWE_DF,Number=1,Type=Integer,Description="Degrees of freedom for Genotype likelihood based Hardy Weinberg Likelihood Ratio Test Statistic">

  HWE       GL based Hardy-Weinberg statistics.

  ##INFO=<ID=FIC,Number=1,Type=Float,Description="Genotype likelihood based Inbreeding Coefficient">

              HWE_LLR   : log likelihood ratio

              HWE_LPVAL : log p-value

              HWE_DF   : degrees of freedom

  AB        GL based Allele Balance.

  FIC       GL based Inbreeding Coefficient

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   usage : vt compute_features for variants [options] <in.vcf>

   usage : vt estimate [options] <in.vcf>

   

   

   options : -s  print site information only without genotypes [false]

   options : -s  print site information only without genotypes [false]

             -o  output VCF/VCF.GZ/BCF file [-]

             -o  output VCF/VCF.GZ/BCF file [-]

             -f  filter expression []

             -f  filter expression []

             -I  File containing list of intervals

             -I  File containing list of intervals