X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bcftools%2Fbcftools.1;h=c6b496867340207585ff6e3a6befa5cf72262c6b;hp=6c7403bea6b8b6ebde3c77a8a1ef55ee890fcd59;hb=9f4bebab2e0917c676ae739b2d05cb22ad6c4ed5;hpb=6a0c6f060a60789b48e10a72b1381f6e54599302 diff --git a/bcftools/bcftools.1 b/bcftools/bcftools.1 index 6c7403b..c6b4968 100644 --- 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. @@ -20,53 +20,57 @@ estimating site allele frequencies and allele frequency spectrums. .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 @@ -74,31 +78,75 @@ 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)