1 .TH bcftools 1 "16 March 2011" "bcftools" "Bioinformatics tools"
4 bcftools - Utilities for the Binary Call Format (BCF) and VCF.
9 bcftools view in.bcf chr2:100-200 > out.vcf
11 bcftools view -vc in.bcf > out.vcf 2> out.afs
15 Bcftools is a toolkit for processing VCF/BCF files, calling variants and
16 estimating site allele frequencies and allele frequency spectrums.
18 .SH COMMANDS AND OPTIONS
49 Convert between BCF and VCF, call variant candidates and estimate allele
54 .B Input/Output Options:
57 Retain all possible alternate alleles at variant sites. By default, the view
58 command discards unlikely alleles.
61 Output in the BCF format. The default is VCF.
64 Sequence dictionary (list of chromosome names) for VCF->BCF conversion [null]
67 Indicate PL is generated by r921 or before (ordering is different).
70 Suppress all individual genotype information.
73 List of sites at which information are outputted [all sites]
76 Skip sites where the REF field is not A/C/G/T
79 Output the QCALL likelihood format
82 List of samples to use. The first column in the input gives the sample names
83 and the second gives the ploidy, which can only be 1 or 2. When the 2nd column
84 is absent, the sample ploidy is assumed to be 2. In the output, the ordering of
85 samples will be identical to the one in
90 The input is VCF instead of BCF.
93 Uncompressed BCF output (force -b).
95 .B Consensus/Variant Calling Options:
98 Call variants using Bayesian inference. This option automatically invokes option
104 is in use, skip loci where the fraction of samples covered by reads is below FLOAT. [0]
107 Perform max-likelihood inference only, including estimating the site allele frequency,
108 testing Hardy-Weinberg equlibrium and testing associations with LRT.
111 Call per-sample genotypes at variant sites (force -c)
114 Ratio of INDEL-to-SNP mutation rate [0.15]
117 A site is considered to be a variant if P(ref|D)<FLOAT [0.5]
120 Prior or initial allele frequency spectrum. If STR can be
124 or the file consisting of error output from a previous variant calling
128 Scaled muttion rate for variant calling [0.001]
131 Output variant sites only (force -c)
133 .B Contrast Calling and Association Test Options:
136 Number of group-1 samples. This option is used for dividing the samples into
137 two groups for contrast SNP calling or association test.
138 When this option is in use, the following VCF INFO will be outputted:
139 PC2, PCHI2 and QCHI2. [0]
142 Number of permutations for association test (effective only with
147 Only perform permutations for P(chi^2)<FLOAT (effective only with
157 Index sorted BCF for random access.
164 .RI [ "in2.bcf " [ ... "]]]"
166 Concatenate BCF files. The input files are required to be sorted and
167 have identical samples appearing in the same order.
170 .SH BCFTOOLS SPECIFIC VCF TAGS
176 Tag Format Description
178 AF1 double Max-likelihood estimate of the site allele frequency (AF) of the first ALT allele
179 CI95 double[2] Equal-tail Bayesian credible interval of AF at the 95% level
180 DP int Raw read depth (without quality filtering)
181 DP4 int[4] # high-quality reference forward bases, ref reverse, alternate for and alt rev bases
182 FQ int Consensus quality. Positive: sample genotypes different; negative: otherwise
183 MQ int Root-Mean-Square mapping quality of covering reads
184 PC2 int[2] Phred probability of AF in group1 samples being larger (,smaller) than in group2
185 PCHI2 double Posterior weighted chi^2 P-value between group1 and group2 samples
186 PV4 double[4] P-value for strand bias, baseQ bias, mapQ bias and tail distance bias
187 QCHI2 int Phred-scaled PCHI2
188 RP int # permutations yielding a smaller PCHI2