extract-snp(1)

NAME
extract-snp - tool to extract dosage values for a given SNP for all or some individuals.

SYNOPSIS
extract-snp -f FILE -s SNPNAME [OPTIONS]

DESCRIPTION
extract-snp extracts the dosage for a SNP for one or more individuals from a file in filevector format (.fvi/.fvd).

OPTIONS

  Required command line options

-f, --file FILE
    Name of the filevector file from which to extract the dosages. This can be either the file with the .fvi or the .fvd extension.

-s, --snp snpname
    Name of the SNP or variant for which to extract the dosages

  Other, non-mandatory options

-i, --id individualID
    Extract the dosage for only one individual (with ID individualID) for the SNP listed with the --snp option.

-I, --listids
    List all ID names in the fv file. If this option is used, any other options are ignored.

-L, --listsnps
    List all SNP names in the fv file. If this option is used, any other options are ignored.

-h, --help
    Print usage information to the screen and exit.

-d, --debug
    Turn on debug mode. This will print a lot of extra output to the screen, for example it lists the names of all individuals and SNPs found in the file.

EXAMPLES
This extracts the dosages for all individuals and saves them in the file dosages.txt:
    extract-snp -f ../checks/inputfiles/mmscore_gen.dose.fvi -s rs70099 > dosages.txt

SEE ALSO
palinear(1), palogist(1), pacoxph(1), probabel(1), and the R package DatABEL.

BUGS
The bugtracker is located at
https://github.com/GenABEL-Project/ProbABEL/issues

AUTHORS
Lennart C. Karssen