-.TH bcftools 1 "2 October 2010" "bcftools" "Bioinformatics tools"
+.TH bcftools 1 "16 March 2011" "bcftools" "Bioinformatics tools"
.SH NAME
.PP
bcftools - Utilities for the Binary Call Format (BCF) and VCF.
.TP 10
.B view
.B bcftools view
-.RB [ \-cbuSAGgHvNQ ]
-.RB [ \-1
-.IR nGroup1 ]
+.RB [ \-AbFGNQSucgv ]
+.RB [ \-D
+.IR seqDict ]
.RB [ \-l
-.IR listFile ]
+.IR listLoci ]
+.RB [ \-s
+.IR listSample ]
+.RB [ \-i
+.IR gapSNPratio ]
.RB [ \-t
.IR mutRate ]
.RB [ \-p
.IR varThres ]
.RB [ \-P
.IR prior ]
+.RB [ \-1
+.IR nGroup1 ]
+.RB [ \-d
+.IR minFrac ]
+.RB [ \-U
+.IR nPerm ]
+.RB [ \-X
+.IR permThres ]
.I in.bcf
.RI [ region ]
Convert between BCF and VCF, call variant candidates and estimate allele
frequencies.
-.B OPTIONS:
.RS
+.TP
+.B Input/Output Options:
+.TP 10
+.B -A
+Retain all possible alternate alleles at variant sites. By default, the view
+command discards unlikely alleles.
.TP 10
.B -b
Output in the BCF format. The default is VCF.
.TP
-.B -c
-Call variants.
+.BI -D \ FILE
+Sequence dictionary (list of chromosome names) for VCF->BCF conversion [null]
.TP
-.B -v
-Output variant sites only (force -c)
-.TP
-.B -g
-Call per-sample genotypes at variant sites (force -c)
-.TP
-.B -u
-Uncompressed BCF output (force -b).
-.TP
-.B -S
-The input is VCF instead of BCF.
-.TP
-.B -A
-Retain all possible alternate alleles at variant sites. By default, this
-command discards unlikely alleles.
+.B -F
+Indicate PL is generated by r921 or before (ordering is different).
.TP
.B -G
Suppress all individual genotype information.
.TP
-.B -H
-Perform Hardy-Weiberg Equilibrium test. This will add computation time, sometimes considerably.
+.BI -l \ FILE
+List of sites at which information are outputted [all sites]
.TP
.B -N
Skip sites where the REF field is not A/C/G/T
.B -Q
Output the QCALL likelihood format
.TP
-.B -f
-Reference-free variant calling mode. In this mode, the prior will be
-folded; a variant is called iff the sample(s) contains at least two
-alleles; the QUAL field in the VCF/BCF output is changed accordingly.
+.BI -s \ FILE
+List of samples to use. The first column in the input gives the sample names
+and the second gives the ploidy, which can only be 1 or 2. When the 2nd column
+is absent, the sample ploidy is assumed to be 2. In the output, the ordering of
+samples will be identical to the one in
+.IR FILE .
+[null]
+.TP
+.B -S
+The input is VCF instead of BCF.
.TP
-.BI "-1 " INT
-Number of group-1 samples. This option is used for dividing input into
-two groups for comparing. A zero value disables this functionality. [0]
+.B -u
+Uncompressed BCF output (force -b).
.TP
-.BI "-l " FILE
-List of sites at which information are outputted [all sites]
+.B Consensus/Variant Calling Options:
+.TP 10
+.B -c
+Call variants using Bayesian inference. This option automatically invokes option
+.BR -e .
.TP
-.BI "-t " FLOAT
-Scaled muttion rate for variant calling [0.001]
+.BI -d \ FLOAT
+When
+.B -v
+is in use, skip loci where the fraction of samples covered by reads is below FLOAT. [0]
+.TP
+.B -e
+Perform max-likelihood inference only, including estimating the site allele frequency,
+testing Hardy-Weinberg equlibrium and testing associations with LRT.
+.TP
+.B -g
+Call per-sample genotypes at variant sites (force -c)
.TP
-.BI "-p " FLOAT
+.BI -i \ FLOAT
+Ratio of INDEL-to-SNP mutation rate [0.15]
+.TP
+.BI -p \ FLOAT
A site is considered to be a variant if P(ref|D)<FLOAT [0.5]
.TP
-.BI "-P " STR
+.BI -P \ STR
Prior or initial allele frequency spectrum. If STR can be
.IR full ,
.IR cond2 ,
.I flat
or the file consisting of error output from a previous variant calling
run.
+.TP
+.BI -t \ FLOAT
+Scaled muttion rate for variant calling [0.001]
+.TP
+.B -v
+Output variant sites only (force -c)
+.TP
+.B Contrast Calling and Association Test Options:
+.TP
+.BI -1 \ INT
+Number of group-1 samples. This option is used for dividing the samples into
+two groups for contrast SNP calling or association test.
+When this option is in use, the following VCF INFO will be outputted:
+PC2, PCHI2 and QCHI2. [0]
+.TP
+.BI -U \ INT
+Number of permutations for association test (effective only with
+.BR -1 )
+[0]
+.TP
+.BI -X \ FLOAT
+Only perform permutations for P(chi^2)<FLOAT (effective only with
+.BR -U )
+[0.01]
.RE
.TP
Concatenate BCF files. The input files are required to be sorted and
have identical samples appearing in the same order.
.RE
+
+.SH BCFTOOLS SPECIFIC VCF TAGS
+
+.TS
+center box;
+cb | cb | cb
+l | l | l .
+Tag Format Description
+_
+AF1 double Max-likelihood estimate of the site allele frequency (AF) of the first ALT allele
+CI95 double[2] Equal-tail Bayesian credible interval of AF at the 95% level
+DP int Raw read depth (without quality filtering)
+DP4 int[4] # high-quality reference forward bases, ref reverse, alternate for and alt rev bases
+FQ int Consensus quality. Positive: sample genotypes different; negative: otherwise
+MQ int Root-Mean-Square mapping quality of covering reads
+PC2 int[2] Phred probability of AF in group1 samples being larger (,smaller) than in group2
+PCHI2 double Posterior weighted chi^2 P-value between group1 and group2 samples
+PV4 double[4] P-value for strand bias, baseQ bias, mapQ bias and tail distance bias
+QCHI2 int Phred-scaled PCHI2
+RP int # permutations yielding a smaller PCHI2
+.TE
projects / samtools.git / blobdiff