FATAL ERROR - Invalid option in handling bFree

[pd3]

I am getting an error from verifyBamID:

$ verifyBamID --free-mix --maxDepth 1000 --precise --ignoreRG --vcf 1000GP_Phase3_snps.vcf.gz --bam input.bam --out test


verifyBamID 1.0.0 -- verify identity and purity of sequence data
(c) 2010 Hyun Min Kang, Goo Jun, and Goncalo Abecasis


The following parameters are available.  Ones with "[]" are in effect:

Available Options
                             Input Files : --vcf [1000GP_Phase3_snps.vcf.gz],
                                           --bam [input.bam],
                                           --subset [], --smID []
                    VCF analysis options : --genoError [1.0e-03],
                                           --minAF [0.01],
                                           --minCallRate [0.50]
   Individuals to compare with chip data : --site, --self, --best
          Chip-free optimization options : --free-none, --free-mix,
                                           --free-refBias, --free-full
          With-chip optimization options : --chip-none, --chip-mix [ON],
                                           --chip-refBias, --chip-full
                    BAM analysis options : --ignoreRG [ON],
                                           --ignoreOverlapPair, --noEOF,
                                           --precise [ON], --minMapQ [10],
                                           --maxDepth [1000], --minQ [13],
                                           --maxQ [40], --grid [0.05]
                 Modeling Reference Bias : --refRef [1.00], --refHet [0.50],
                                           --refAlt [0.00]
                          Output options : --out [test],
                                           --verbose

verifyBamID 1.1.3 -- verify identity and purity of sequence data
(c) 2010-2014 Hyun Min Kang, Goo Jun, and Goncalo Abecasis

WARNING - 
--self option was autotomatically turned on by default. Specify --best option if you wanted to check across all possible samples in the VCF

FATAL ERROR - 
Invalid option in handling bFree

[pd3]

The problem was in giving the --free-mix option. It turns out that the option toggles the selection: by default it is on, giving it once turns it off, giving it twice turns it on again.

This is far from obvious and the error message is not informative, had to consult the source code. It would be nice if the program exited immediately before processing the whole file, thought there was something wrong with my data.