Plugin fill-tags

This plugin can be used to compute and fill various INFO tags:

INFO/AC        Number:A  Type:Integer  ..  Allele count in genotypes
INFO/AC_Hom    Number:A  Type:Integer  ..  Allele counts in homozygous genotypes
INFO/AC_Het    Number:A  Type:Integer  ..  Allele counts in heterozygous genotypes
INFO/AC_Hemi   Number:A  Type:Integer  ..  Allele counts in hemizygous genotypes
INFO/AF        Number:A  Type:Float    ..  Allele frequency
INFO/AN        Number:1  Type:Integer  ..  Total number of alleles in called genotypes
INFO/ExcHet    Number:A  Type:Float    ..  Test excess heterozygosity; 1=good, 0=bad
INFO/END       Number:1  Type:Integer  ..  End position of the variant
INFO/F_MISSING Number:1  Type:Float    ..  Fraction of missing genotypes (all samples, experimental)
INFO/HWE       Number:A  Type:Float    ..  HWE test (PMID:15789306); 1=good, 0=bad
INFO/MAF       Number:A  Type:Float    ..  Minor Allele frequency
INFO/NS        Number:1  Type:Integer  ..  Number of samples with data
INFO/TYPE      Number:.  Type:String   ..  The record type (REF,SNP,MNP,INDEL,etc)
FORMAT/VAF     Number:A  Type:Float    ..  The fraction of reads with the alternate allele, requires FORMAT/AD
FORMAT/VAF1    Number:1  Type:Float    ..  The same as FORMAT/VAF but for all alternate alleles cumulatively
TAG=func(TAG)  Number:1  Type:Integer  ..  Experimental support for user-defined expressions such as "DP=sum(DP)". This is currently very basic, to be extended.

By default the values are calculated across all samples, but also per-population values can be calculated. For this, provide a file with the list of samples in the first column and a comma-separated list of populations in the second column. The file can look for example like this:

Sample1     Group1
Sample2     Group1,Group2
Sample3     Group2

The list of plugin-specific options can be obtained by running bcftools +fill-tags -h, which will print the following usage page:

About: Set INFO tags AF, AC, AC_Hemi, AC_Hom, AC_Het, AN, ExcHet, HWE, MAF, NS
       FORMAT tag VAF, custom INFO/TAG=func(FMT/TAG).
       See examples below, run with -l for detailed description.

Usage: bcftools +fill-tags [General Options] -- [Plugin Options]
Options:
   run "bcftools plugin" for a list of common options

Plugin options:
   -d, --drop-missing          do not count half-missing genotypes "./1" as hemizygous
   -l, --list-tags             list available tags with description
   -t, --tags LIST             list of output tags. By default, all tags are filled.
   -S, --samples-file FILE     list of samples (first column) and comma-separated list of populations (second column)

Examples:
   # Print a detailed list of available tags
   bcftools +fill-tags -- -l

   # Fill INFO/AN and INFO/AC
   bcftools +fill-tags in.bcf -Ob -o out.bcf -- -t AN,AC

   # Fill all available tags
   bcftools +fill-tags in.bcf -Ob -o out.bcf -- -t all

   # Calculate HWE for sample groups (possibly multiple) read from a file
   bcftools +fill-tags in.bcf -Ob -o out.bcf -- -S sample-group.txt -t HWE

   # Calculate total read depth (INFO/DP) from per-sample depths (FORMAT/DP)
   bcftools +fill-tags in.bcf -Ob -o out.bcf -- -t 'DP=sum(DP)'

    # Annotate with allelic fraction
    bcftools +fill-tags in.bcf -Ob -o out.bcf -- -t FORMAT/VAF\n"

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