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
47 Convert between BCF and VCF, call variant candidates and estimate allele
52 .B Input/Output Options:
55 Retain all possible alternate alleles at variant sites. By default, the view
56 command discards unlikely alleles.
59 Output in the BCF format. The default is VCF.
62 Sequence dictionary (list of chromosome names) for VCF->BCF conversion [null]
65 Indicate PL is generated by r921 or before (ordering is different).
68 Suppress all individual genotype information.
71 List of sites at which information are outputted [all sites]
74 Skip sites where the REF field is not A/C/G/T
77 Output the QCALL likelihood format
80 List of samples to use. In the output, the ordering of samples will be identical
86 The input is VCF instead of BCF.
89 Uncompressed BCF output (force -b).
91 .B Consensus/Variant Calling Options:
97 Call per-sample genotypes at variant sites (force -c)
100 Ratio of INDEL-to-SNP mutation rate [0.15]
103 A site is considered to be a variant if P(ref|D)<FLOAT [0.5]
106 Prior or initial allele frequency spectrum. If STR can be
110 or the file consisting of error output from a previous variant calling
114 Scaled muttion rate for variant calling [0.001]
117 Output variant sites only (force -c)
119 .B Contrast Calling and Association Test Options:
122 Number of group-1 samples. This option is used for dividing the samples into
123 two groups for contrast SNP calling or association test.
124 When this option is in use, the following VCF INFO will be outputted:
125 PC2, PCHI2 and QCHI2. [0]
128 Number of permutations for association test (effective only with
133 Only perform permutations for P(chi^2)<FLOAT (effective only with
143 Index sorted BCF for random access.
150 .RI [ "in2.bcf " [ ... "]]]"
152 Concatenate BCF files. The input files are required to be sorted and
153 have identical samples appearing in the same order.
156 .SH BCFTOOLS SPECIFIC VCF TAGS
162 Tag Format Description
164 AF1 double Max-likelihood estimate of the site allele frequency (AF) of the first ALT allele
165 CI95 double[2] Equal-tail Bayesian credible interval of AF at the 95% level
166 DP int Raw read depth (without quality filtering)
167 DP4 int[4] # high-quality reference forward bases, ref reverse, alternate for and alt rev bases
168 FQ int Consensus quality. Positive: sample genotypes different; negative: otherwise
169 MQ int Root-Mean-Square mapping quality of covering reads
170 PC2 int[2] Phred probability of AF in group1 samples being larger (,smaller) than in group2
171 PCHI2 double Posterior weighted chi^2 P-value between group1 and group2 samples
172 PV4 double[4] P-value for strand bias, baseQ bias, mapQ bias and tail distance bias
173 QCHI2 int Phred-scaled PCHI2
174 RP int # permutations yielding a smaller PCHI2