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¶

LICENSE¶

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

AUTHORS¶

Erik Garrison and vcflib contributors.