+++ /dev/null
-.TH bcftools 1 "16 March 2011" "bcftools" "Bioinformatics tools"
-.SH NAME
-.PP
-bcftools - Utilities for the Binary Call Format (BCF) and VCF.
-.SH SYNOPSIS
-.PP
-bcftools index in.bcf
-.PP
-bcftools view in.bcf chr2:100-200 > out.vcf
-.PP
-bcftools view -vc in.bcf > out.vcf 2> out.afs
-
-.SH DESCRIPTION
-.PP
-Bcftools is a toolkit for processing VCF/BCF files, calling variants and
-estimating site allele frequencies and allele frequency spectrums.
-
-.SH COMMANDS AND OPTIONS
-
-.TP 10
-.B view
-.B bcftools view
-.RB [ \-AbFGNQSucgv ]
-.RB [ \-D
-.IR seqDict ]
-.RB [ \-l
-.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.
-
-.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
-.BI -D \ FILE
-Sequence dictionary (list of chromosome names) for VCF->BCF conversion [null]
-.TP
-.B -F
-Indicate PL is generated by r921 or before (ordering is different).
-.TP
-.B -G
-Suppress all individual genotype information.
-.TP
-.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
-.TP
-.B -Q
-Output the QCALL likelihood format
-.TP
-.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
-.B -u
-Uncompressed BCF output (force -b).
-.TP
-.B Consensus/Variant Calling Options:
-.TP 10
-.B -c
-Call variants using Bayesian inference. This option automatically invokes option
-.BR -e .
-.TP
-.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 -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
-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
-.B index
-.B bcftools index
-.I in.bcf
-
-Index sorted BCF for random access.
-.RE
-
-.TP
-.B cat
-.B bcftools cat
-.I in1.bcf
-.RI [ "in2.bcf " [ ... "]]]"
-
-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