vcfgenotypes.md

% VCFGENOTYPES(1) vcfgenotypes (vcflib) | vcfgenotypes (VCF statistics) % Erik Garrison and vcflib contributors

NAME

vcfgenotypes

SYNOPSIS

vcfgenotypes

DESCRIPTION

Report the genotypes for each sample, for each variant in the VCF. Convert the numerical represenation of genotypes provided by the GT field to a human-readable genotype format.

OPTIONS

EXAMPLES

Example:

      **vcfgenotypes** samples/sample.vcf

19      111     A       C       A,C     NA00001:A/A     NA00002:A/A     NA00003:A/C
19      112     A       G       A,G     NA00001:A/A     NA00002:A/A     NA00003:A/G
20      14370   G       A       G,A     NA00001:G/G     NA00002:G/A     NA00003:A/A
20      17330   T       A       T,A     NA00001:T/T     NA00002:T/A     NA00003:T/T
20      1110696 A       G,T     A,G,T   NA00001:G/T     NA00002:G/T     NA00003:T/T
20      1230237 T       .       T,.     NA00001:T/T     NA00002:T/T     NA00003:T/T
20      1234567 G       GA,GAC  G,GA,GAC        NA00001:G/GA    NA00002:G/GAC   NA00003:GA/GA
20      1235237 T       .       T,.     NA00001:T/T     NA00002:T/T     NA00003:./.
X       10      AC      A,ATG   AC,A,ATG        NA00001:AC      NA00002:AC/A    NA00003:AC/ATG

Type: statistics

EXIT VALUES

0 : Success

not 0 : Failure

SEE ALSO

vcflib(1)

OTHER

Source code

vcfgenotypes.cpp

LICENSE

Copyright 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2024 (C) Pjotr Prins.