This tool converts BCF files into VCF files using BCFtools view from the SAMtools set of utilities.
bcftools view [options] <in.vcf.gz> [region1 [...]]
-G, --drop-genotypes
drop individual genotype information (after subsetting if -s option is set)
-h, --header-only
output the VCF header only
-H, --no-header
suppress the header in VCF output
-l, --compression-level [0-9]
compression level. 0 stands for uncompressed, 1 for best speed and 9 for best compression.
--no-version
-O, --output-type b|u|z|v
-o, --output-file FILE: output file name. If not present, the default is to print to standard output (stdout).
-r, --regions chr|chr:pos|chr:from-to|chr:from-[,…]
-R, --regions-file file
-t, --targets chr|chr:pos|chr:from-to|chr:from-[,…]
-T, --targets-file file
--threads INT
-a, --trim-alt-alleles
trim alternate alleles not seen in subset. Type A, G and R INFO and FORMAT fields will also be trimmed
--force-samples
only warn about unknown subset samples
-I, --no-update
do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)
-s, --samples LIST
-S, --samples-file FILE
-c, --min-ac INT[:nref|:alt1|:minor|:major|:'nonmajor']
minimum allele count (INFO/AC) of sites to be printed. Specifying the type of allele is optional and can be set to non-reference (nref, the default), 1st alternate (alt1), the least frequent (minor), the most frequent (major) or sum of all but the most frequent (nonmajor) alleles.
-C, --max-ac INT[:nref|:alt1|:minor|:'major'|:'nonmajor']
maximum allele count (INFO/AC) of sites to be printed. Specifying the type of allele is optional and can be set to non-reference (nref, the default), 1st alternate (alt1), the least frequent (minor), the most frequent (major) or sum of all but the most frequent (nonmajor) alleles.
-e, --exclude EXPRESSION
exclude sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.
-f, --apply-filters LIST
-g, --genotype [^][hom|het|miss]
include only sites with one or more homozygous (hom), heterozygous (het) or missing (miss) genotypes. When prefixed with ^, the logic is reversed; thus ^het excludes sites with heterozygous genotypes.
-i, --include EXPRESSION
include sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.
-k, --known
print known sites only (ID column is not ".")
-m, --min-alleles INT
print sites with at least INT alleles listed in REF and ALT columns
-M, --max-alleles INT
print sites with at most INT alleles listed in REF and ALT columns. Use -m2 -M2 -v snps to only view biallelic SNPs.
-n, --novel
print novel sites only (ID column is ".")
-p, --phased
print sites where all samples are phased. Haploid genotypes are considered phased. Missing genotypes considered unphased unless the phased bit is set.
-P, --exclude-phased
exclude sites where all samples are phased
-q, --min-af FLOAT[:nref|:alt1|:minor|:major|:nonmajor]
minimum allele frequency (INFO/AC / INFO/AN) of sites to be printed. Specifying the type of allele is optional and can be set to non-reference (nref, the default), 1st alternate (alt1), the least frequent (minor), the most frequent (major) or sum of all but the most frequent (nonmajor) alleles.
-Q, --max-af FLOAT[:nref|:alt1|:minor|:major|:nonmajor]
maximum allele frequency (INFO/AC / INFO/AN) of sites to be printed. Specifying the type of allele is optional and can be set to non-reference (nref, the default), 1st alternate (alt1), the least frequent (minor), the most frequent (major) or sum of all but the most frequent (nonmajor) alleles.
-u, --uncalled
print sites without a called genotype
-U, --exclude-uncalled
exclude sites without a called genotype
-v, --types snps|indels|mnps|other
comma-separated list of variant types to select. Site is selected if any of the ALT alleles is of the type requested. Types are determined by comparing the REF and ALT alleles in the VCF record not INFO tags like INFO/INDEL or INFO/VT. Use --include to select based on INFO tags.
-V, --exclude-types snps|indels|mnps|other
comma-separated list of variant types to exclude. Site is excluded if any of the ALT alleles is of the type requested. Types are determined by comparing the REF and ALT alleles in the VCF record not INFO tags like INFO/INDEL or INFO/VT. Use --exclude to exclude based on INFO tags.
-x, --private
print sites where only the subset samples carry an non-reference allele. Requires --samples or --samples-file.
-X, --exclude-private
exclude sites where only the subset samples carry an non-reference allele