bcftools version

[crazyhottommy]

Hi I have a lot of bam files, and I want to generate the vcf files first by samtools.

bcftools view -cg gives me error. I think the version of bcftools matters.

my bcftools:

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]
          --no-version                  do not append version and command line to the header
    -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
        --threads <int>                 number of extra (de)compression threads [0]

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,ref,bnd,other [null]
    -x/X, --private/--exclude-private           select/exclude sites where the non-reference alleles are exclusive (private) to the subset samples

Thank you!

[sejooning]

Hi,

Former SNP/INDEL calling function of bcftools "view" has changed to "call" in the latest version of bcftools. You may use "bcftools call -c > outfile" for the latest bcftools instead of "bcftools view -cg > outfile".

You may find more information below, https://samtools.github.io/bcftools/bcftools.html

Thank you, Best, Sejoon Lee

[crazyhottommy]

Thanks!