+ /mmfs1/gscratch/srlab/nextflow/bin/miniforge/bin/bcftools --version
bcftools 1.22
Using htslib 1.22.1
Copyright (C) 2025 Genome Research Ltd.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
+ echo 'Hard filtering variants'
Hard filtering variants
+ /mmfs1/gscratch/srlab/nextflow/bin/miniforge/bin/bcftools filter -e 'INFO/FS > 60.0' --set-filter FS -e 'INFO/QD < 2.0' --set-filter QD -e 'QUAL < 30.0' --set-filter QUAL30 -e 'INFO/SOR > 3.0' --set-filter SOR3 -e 'INFO/DP < 15' --set-filter DP15 -e 'INFO/DP > 150' --set-filter DP150 -e 'INFO/AF < 0.30' --set-filter AF30 -Oz -o merged-filtered.vcf.gz merged.vcf.gz
filter: unrecognized option '--set-filter'

About:   Apply fixed-threshold filters.
Usage:   bcftools filter [options] <in.vcf.gz>

Options:
    -e, --exclude EXPR             Exclude sites for which the expression is true (see man page for details)
    -g, --SnpGap INT[:TYPE]        Filter SNPs within <int> base pairs of an indel (the default) or any combination of indel,mnp,bnd,other,overlap
    -G, --IndelGap INT             Filter clusters of indels separated by <int> or fewer base pairs allowing only one to pass
    -i, --include EXPR             Include only sites for which the expression is true (see man page for details
        --mask [^]REGION           Soft filter regions, "^" to negate
    -M, --mask-file [^]FILE        Soft filter regions listed in a file, "^" to negate
        --mask-overlap 0|1|2       Mask if POS in the region (0), record overlaps (1), variant overlaps (2) [1]
    -m, --mode [+x]                "+": do not replace but add to existing FILTER; "x": reset filters at sites which pass
        --no-version               Do not append version and command line to the header
    -o, --output FILE              Write output to a file [standard output]
    -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]
    -r, --regions REGION           Restrict to comma-separated list of regions
    -R, --regions-file FILE        Restrict to regions listed in a file
        --regions-overlap 0|1|2    Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]
    -s, --soft-filter STRING       Annotate FILTER column with <string> or unique filter name ("Filter%d") made up by the program ("+")
    -S, --set-GTs .|0              Set genotypes of failed samples to missing (.) or ref (0)
    -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
        --targets-overlap 0|1|2    Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]
        --threads INT              Use multithreading with <int> worker threads [0]
    -v, --verbosity INT            Verbosity level
    -W, --write-index[=FMT]        Automatically index the output files [off]