Uploaded samtools_0.1.16-1_amd64.changes.

[samtools.git] / bcftools / bcftools.1

diff --git a/bcftools/bcftools.1 b/bcftools/bcftools.1
index ebff30134002500216c18a1e9eeee3e8a8dba8a8..c6b496867340207585ff6e3a6befa5cf72262c6b 100644 (file)
--- a/bcftools/bcftools.1
+++ b/bcftools/bcftools.1
@@ -1,4 +1,4 @@
-.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.
 .SH NAME
 .PP
 bcftools - Utilities for the Binary Call Format (BCF) and VCF.


@@ -20,53 +20,57 @@ estimating site allele frequencies and allele frequency spectrums.
 .TP 10
 .B view
 .B bcftools view
 .TP 10
 .B view
 .B bcftools view

-.RB [ \-cbuSAGgHvNQ ]
-.RB [ \-1
-.IR nGroup1 ]
+.RB [ \-AbFGNQSucgv ]
+.RB [ \-D
+.IR seqDict ]

 .RB [ \-l
 .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 [ \-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.
 
 .I in.bcf
 .RI [ region ]
 
 Convert between BCF and VCF, call variant candidates and estimate allele
 frequencies.
 

-.B OPTIONS:

 .RS
 .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
 .TP 10
 .B -b
 Output in the BCF format. The default is VCF.
 .TP

-.B -c
-Call variants.
-.TP
-.B -v
-Output variant sites only (force -c)
-.TP
-.B -g
-Call per-sample genotypes at variant sites (force -c)
+.BI -D \ FILE
+Sequence dictionary (list of chromosome names) for VCF->BCF conversion [null]

 .TP
 .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
 .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
 .TP
 .B -N
 Skip sites where the REF field is not A/C/G/T


@@ -74,26 +78,75 @@ Skip sites where the REF field is not A/C/G/T
 .B -Q
 Output the QCALL likelihood format
 .TP
 .B -Q
 Output the QCALL likelihood format
 .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]
+.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
 .TP

-.BI "-l " FILE
-List of sites at which information are outputted [all sites]
+.B -S
+The input is VCF instead of BCF.

 .TP
 .TP

-.BI "-t " FLOAT
-Scaled muttion rate for variant calling [0.001]
+.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
 .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
 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.
 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
 .RE
 
 .TP


@@ -113,3 +166,24 @@ Index sorted BCF for random access.
 Concatenate BCF files. The input files are required to be sorted and
 have identical samples appearing in the same order.
 .RE
 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