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1 .TH bcftools 1 "16 March 2011" "bcftools" "Bioinformatics tools"
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2 .SH NAME
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3 .PP
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4 bcftools - Utilities for the Binary Call Format (BCF) and VCF.
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5 .SH SYNOPSIS
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6 .PP
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7 bcftools index in.bcf
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8 .PP
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9 bcftools view in.bcf chr2:100-200 > out.vcf
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10 .PP
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11 bcftools view -vc in.bcf > out.vcf 2> out.afs
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12
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13 .SH DESCRIPTION
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14 .PP
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15 Bcftools is a toolkit for processing VCF/BCF files, calling variants and
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16 estimating site allele frequencies and allele frequency spectrums.
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17
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18 .SH COMMANDS AND OPTIONS
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19
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20 .TP 10
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21 .B view
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22 .B bcftools view
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23 .RB [ \-AbFGNQSucgv ]
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24 .RB [ \-D
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25 .IR seqDict ]
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26 .RB [ \-l
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27 .IR listLoci ]
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28 .RB [ \-s
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29 .IR listSample ]
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30 .RB [ \-i
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31 .IR gapSNPratio ]
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32 .RB [ \-t
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33 .IR mutRate ]
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34 .RB [ \-p
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35 .IR varThres ]
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36 .RB [ \-P
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37 .IR prior ]
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38 .RB [ \-1
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39 .IR nGroup1 ]
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40 .RB [ \-d
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41 .IR minFrac ]
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42 .RB [ \-U
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43 .IR nPerm ]
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44 .RB [ \-X
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45 .IR permThres ]
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46 .I in.bcf
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47 .RI [ region ]
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48
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49 Convert between BCF and VCF, call variant candidates and estimate allele
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50 frequencies.
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51
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52 .RS
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53 .TP
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54 .B Input/Output Options:
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55 .TP 10
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56 .B -A
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57 Retain all possible alternate alleles at variant sites. By default, the view
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58 command discards unlikely alleles.
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59 .TP 10
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60 .B -b
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61 Output in the BCF format. The default is VCF.
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62 .TP
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63 .BI -D \ FILE
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64 Sequence dictionary (list of chromosome names) for VCF->BCF conversion [null]
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65 .TP
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66 .B -F
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67 Indicate PL is generated by r921 or before (ordering is different).
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68 .TP
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69 .B -G
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70 Suppress all individual genotype information.
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71 .TP
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72 .BI -l \ FILE
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73 List of sites at which information are outputted [all sites]
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74 .TP
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75 .B -N
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76 Skip sites where the REF field is not A/C/G/T
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77 .TP
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78 .B -Q
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79 Output the QCALL likelihood format
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80 .TP
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81 .BI -s \ FILE
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82 List of samples to use. The first column in the input gives the sample names
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83 and the second gives the ploidy, which can only be 1 or 2. When the 2nd column
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84 is absent, the sample ploidy is assumed to be 2. In the output, the ordering of
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85 samples will be identical to the one in
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86 .IR FILE .
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87 [null]
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88 .TP
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89 .B -S
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90 The input is VCF instead of BCF.
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91 .TP
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92 .B -u
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93 Uncompressed BCF output (force -b).
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94 .TP
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95 .B Consensus/Variant Calling Options:
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96 .TP 10
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97 .B -c
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98 Call variants using Bayesian inference. This option automatically invokes option
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99 .BR -e .
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100 .TP
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101 .BI -d \ FLOAT
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102 When
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103 .B -v
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104 is in use, skip loci where the fraction of samples covered by reads is below FLOAT. [0]
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105 .TP
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106 .B -e
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107 Perform max-likelihood inference only, including estimating the site allele frequency,
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108 testing Hardy-Weinberg equlibrium and testing associations with LRT.
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109 .TP
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110 .B -g
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111 Call per-sample genotypes at variant sites (force -c)
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112 .TP
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113 .BI -i \ FLOAT
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114 Ratio of INDEL-to-SNP mutation rate [0.15]
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115 .TP
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116 .BI -p \ FLOAT
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117 A site is considered to be a variant if P(ref|D)<FLOAT [0.5]
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118 .TP
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119 .BI -P \ STR
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120 Prior or initial allele frequency spectrum. If STR can be
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121 .IR full ,
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122 .IR cond2 ,
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123 .I flat
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124 or the file consisting of error output from a previous variant calling
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125 run.
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126 .TP
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127 .BI -t \ FLOAT
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128 Scaled muttion rate for variant calling [0.001]
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129 .TP
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130 .B -v
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131 Output variant sites only (force -c)
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132 .TP
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133 .B Contrast Calling and Association Test Options:
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134 .TP
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135 .BI -1 \ INT
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136 Number of group-1 samples. This option is used for dividing the samples into
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137 two groups for contrast SNP calling or association test.
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138 When this option is in use, the following VCF INFO will be outputted:
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139 PC2, PCHI2 and QCHI2. [0]
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140 .TP
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141 .BI -U \ INT
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142 Number of permutations for association test (effective only with
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143 .BR -1 )
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144 [0]
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145 .TP
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146 .BI -X \ FLOAT
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147 Only perform permutations for P(chi^2)<FLOAT (effective only with
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148 .BR -U )
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149 [0.01]
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150 .RE
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151
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152 .TP
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153 .B index
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154 .B bcftools index
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155 .I in.bcf
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156
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157 Index sorted BCF for random access.
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158 .RE
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159
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160 .TP
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161 .B cat
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162 .B bcftools cat
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163 .I in1.bcf
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164 .RI [ "in2.bcf " [ ... "]]]"
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165
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166 Concatenate BCF files. The input files are required to be sorted and
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167 have identical samples appearing in the same order.
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168 .RE
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169
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170 .SH BCFTOOLS SPECIFIC VCF TAGS
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171
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172 .TS
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173 center box;
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174 cb | cb | cb
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175 l | l | l .
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176 Tag Format Description
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177 _
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178 AF1 double Max-likelihood estimate of the site allele frequency (AF) of the first ALT allele
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179 CI95 double[2] Equal-tail Bayesian credible interval of AF at the 95% level
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180 DP int Raw read depth (without quality filtering)
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181 DP4 int[4] # high-quality reference forward bases, ref reverse, alternate for and alt rev bases
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182 FQ int Consensus quality. Positive: sample genotypes different; negative: otherwise
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183 MQ int Root-Mean-Square mapping quality of covering reads
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184 PC2 int[2] Phred probability of AF in group1 samples being larger (,smaller) than in group2
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185 PCHI2 double Posterior weighted chi^2 P-value between group1 and group2 samples
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186 PV4 double[4] P-value for strand bias, baseQ bias, mapQ bias and tail distance bias
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187 QCHI2 int Phred-scaled PCHI2
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188 RP int # permutations yielding a smaller PCHI2
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189 .TE
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