vcfstats1

Usage

Overview

Prints statistics about variants in the input VCF file.

Options

    -r, --region          specify a region on which to target the stats, requires a BGZF
                          compressed file which has been indexed with tabix.  any number of
                          regions may be specified.
    -a, --add-info        add the statistics intermediate information to the VCF file,
                          writing out VCF records instead of summary statistics
    -t, --add-type        only add the type= field to the info (faster than -a)
    -l, --no-length-frequency    don't out the indel and mnp length-frequency spectra
    -m, --match-score N          match score for SW algorithm
    -x, --mismatch-score N       mismatch score for SW algorithm
    -o, --gap-open-penalty N     gap open penalty for SW algorithm
    -e, --gap-extend-penalty N   gap extension penalty for SW algorithm
Type: statistics

Exit status

0

Success

not 0

Failure

Other