Thanks for the reply. I will give bcftools call a try.

Yes, I was trying to use the command bcftools view -bvcg ..., but it seem those were the valid options for an older version of bcftools.

I found this list of options for bcftools view (an old version, which explained the -bvcg to me):

Usage: bcftools view [options] <in.bcf> [reg]

Input/output options:

       -A        keep all possible alternate alleles at variant sites
       -b        output BCF instead of VCF
       -D FILE   sequence dictionary for VCF->BCF conversion [null]
       -F        PL generated by r921 or before (which generate old ordering)
       -G        suppress all individual genotype information
       -l FILE   list of sites (chr pos) or regions (BED) to output [all sites]
       -L        calculate LD for adjacent sites
       -N        skip sites where REF is not A/C/G/T
       -Q        output the QCALL likelihood format
       -s FILE   list of samples to use [all samples]
       -S        input is VCF
       -u        uncompressed BCF output (force -b)

Consensus/variant calling options:

       -c        SNP calling (force -e)
       -d FLOAT  skip loci where less than FLOAT fraction of samples covered [0]
       -e        likelihood based analyses
       -g        call genotypes at variant sites (force -c)
       -i FLOAT  indel-to-substitution ratio [-1]
       -I        skip indels
       -m FLOAT  alternative model for multiallelic and rare-variant calling, include if P(chi^2)>=FLOAT
       -p FLOAT  variant if P(ref|D)<FLOAT [0.5]
       -P STR    type of prior: full, cond2, flat [full]
       -t FLOAT  scaled substitution mutation rate [0.001]
       -T STR    constrained calling; STR can be: pair, trioauto, trioxd and trioxs (see manual) [null]
       -v        output potential variant sites only (force -c)

Contrast calling and association test options:

       -1 INT    number of group-1 samples [0]
       -C FLOAT  posterior constrast for LRT<FLOAT and P(ref|D)<0.5 [1]
       -U INT    number of permutations for association testing (effective with -1) [0]
       -X FLOAT  only perform permutations for P(chi^2)<FLOAT [0.01]

but the version 1.2 bcftools view options are :

$ bcftools view

About:   VCF/BCF conversion, view, subset and filter VCF/BCF files.
Usage:   bcftools view [options] <in.vcf.gz> [region1 [...]]

Output options:
    -G,   --drop-genotypes              drop individual genotype information (after subsetting if -s option set)
    -h/H, --header-only/--no-header     print the header only/suppress the header in VCF output
    -l,   --compression-level [0-9]     compression level: 0 uncompressed, 1 best speed, 9 best compression [-1]
    -o,   --output-file <file>          output file name [stdout]
    -O,   --output-type <b|u|z|v>       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
    -t, --targets [^]<region>           similar to -r but streams rather than index-jumps. Exclude regions with "^" prefix
    -T, --targets-file [^]<file>        similar to -R but streams rather than index-jumps. Exclude regions with "^" prefix

Subset options:
    -a, --trim-alt-alleles        trim alternate alleles not seen in the subset
    -I, --no-update               do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)
    -s, --samples [^]<list>       comma separated list of samples to include (or exclude with "^" prefix)
    -S, --samples-file [^]<file>  file of samples to include (or exclude with "^" prefix)
        --force-samples           only warn about unknown subset samples

Filter options:
    -c/C, --min-ac/--max-ac <int>[:<type>]      minimum/maximum count for non-reference (nref), 1st alternate (alt1), least frequent
                                                   (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles [nref]
    -f,   --apply-filters <list>                require at least one of the listed FILTER strings (e.g. "PASS,.")
    -g,   --genotype [^]<hom|het|miss>          require one or more hom/het/missing genotype or, if prefixed with "^", exclude sites with hom/het/missing genotypes
    -i/e, --include/--exclude <expr>            select/exclude sites for which the expression is true (see man page for details)
    -k/n, --known/--novel                       select known/novel sites only (ID is not/is '.')
    -m/M, --min-alleles/--max-alleles <int>     minimum/maximum number of alleles listed in REF and ALT (e.g. -m2 -M2 for biallelic sites)
    -p/P, --phased/--exclude-phased             select/exclude sites where all samples are phased
    -q/Q, --min-af/--max-af <float>[:<type>]    minimum/maximum frequency for non-reference (nref), 1st alternate (alt1), least frequent
                                                   (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles [nref]
    -u/U, --uncalled/--exclude-uncalled         select/exclude sites without a called genotype
    -v/V, --types/--exclude-types <list>        select/exclude comma-separated list of variant types: snps,indels,mnps,other [null]
    -x/X, --private/--exclude-private           select/exclude sites where the non-reference alleles are exclusive (private) to the subset samples

So just trying to find the new options variable that will get me the same output.

Hi Evgeniia,

Gave bcftools call a try and it worked for me.

Thanks for your help.

Eddie