atomize option does not appear in bcftools norm

[jcasadogp]

Hello,

I am working with bcftools in a Conda environment and I have version 1.5. I am trying to use the --atomize, -a command, which I have read that was introduced in bcftools version 1.12.

When I try to run this command,bcftools norm -a -f $REF_GENOME results/02_vcf/snps.vcf.gz I get the following message:

bcftools: invalid option -- a

About:   Left-align and normalize indels; check if REF alleles match the reference;
         split multiallelic sites into multiple rows; recover multiallelics from
         multiple rows.
Usage:   bcftools norm [options] <in.vcf.gz>

Options:
    -c, --check-ref <e|w|x|s>         check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites [e]
    -D, --remove-duplicates           remove duplicate lines of the same type.
    -d, --rm-dup <type>               remove duplicate snps|indels|both|any
    -f, --fasta-ref <file>            reference sequence (MANDATORY)
    -m, --multiallelics <-|+>[type]   split multiallelics (-) or join biallelics (+), type: snps|indels|both|any [both]
        --no-version                  do not append version and command line to the header
    -N, --do-not-normalize            do not normalize indels (with -m or -c s)
    -o, --output <file>               write output to a file [standard output]
    -O, --output-type <type>          'b' compressed BCF; 'u' uncompressed BCF; 'z' compressed VCF; 'v' uncompressed VCF [v]
    -r, --regions <region>            restrict to comma-separated list of regions
    -R, --regions-file <file>         restrict to regions listed in a file
    -s, --strict-filter               when merging (-m+), merged site is PASS only if all sites being merged PASS
    -t, --targets <region>            similar to -r but streams rather than index-jumps
    -T, --targets-file <file>         similar to -R but streams rather than index-jumps
        --threads <int>               number of extra (de)compression threads [0]
    -w, --site-win <int>              buffer for sorting lines which changed position during realignment [1000]

I observe that there are fewer options that the ones indicated in the documentation, but I have found no one relating this kind of error.

Any idea of how I can solve this?

Thank you in advance!

[jkbonfield]

We use semantic versioning of X.Y or X.Y.Z where X, Y and Z are all indepentent numbers. Hence "1.12" is major version 1, minor version 12. It's not just a fraction of 1.5 > 1.12.

Basically if you update to the latest version (1.18) then it should work.

[jcasadogp]

Thank you @jkbonfield, I was so stuck that did not notice that simple thing!