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1 Beta Release 0.1.19 (15 March, 2013)
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2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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3
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4 Notable changes in samtools and bcftools:
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5
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6 * The latest source code and development moved to github,
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7 http://github.com/samtools/samtools
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8
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9 * Many important bugfixes and contributions by many people. Thanks to all!
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10
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11 * Performance improvements (multi-threading)
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12
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13 * Important changes in calling, see
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14 - samtools mpileup -p
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15 - bcftools view -m
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16
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17 * New annotations useful for filtering (RPB, HWE, QBD, MDV)
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18
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19 * New tools, bamcheck and plot-bamcheck
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20
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21 * New features in samtools tview
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22
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23 * And much more..
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24
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25 For a detailed list of commits, please see
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26 http://github.com/samtools/samtools/commits/master
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27
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28 (0.1.19: 15 March 2013, commit 96b5f2294ac0054230e88913c4983d548069ea4e)
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29
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30
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31 Beta Release 0.1.18 (2 September, 2011)
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32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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33
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34 Notable changes in samtools:
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35
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36 * Support the new =/X CIGAR operators (by Peter Cock).
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37
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38 * Allow to subsample BAM while keeping the pairing intact (view -s).
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39
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40 * Implemented variant distance bias as a new filter (by Petr Danecek).
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41
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42 * Bugfix: huge memory usage during indexing
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43
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44 * Bugfix: use of uninitialized variable in mpileup (rare)
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45
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46 * Bugfix: wrong BAQ probability (rare)
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47
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48 Notable changes in bcftools:
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49
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50 * Support indel in the contrast caller.
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51
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52 * Bugfix: LRT2=nan in rare cases
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53
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54 (0.1.18: 2 September 2011, r982:295)
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55
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56
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57
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58 Beta Release 0.1.17 (6 July, 2011)
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59 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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60
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61 With the maturity of `mpileup' and the lack of update in the `pileup' command,
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62 the `pileup' command is now formally dropped. Most of the pileup functionality,
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63 such as outputting mapping quality and read positions, have been added
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64 `mpileup'.
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65
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66 Since this release, `bcftools view' is able to perform contrast SNP calling
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67 (option -T) for discovering de novo and/or somatic mutations between a pair of
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68 samples or in a family trio. Potential mutations are scored by a log likelihood
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69 ratio, which is very simple in math, but should be comparable to more
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70 sophisticated methods. Note that getting the score is only the very first step.
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71 A lot more need to be done to reduce systematical errors due to mapping and
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72 reference errors and structural variations.
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73
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74 Other notable changes in samtools:
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75
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76 * Improved sorting order checking during indexing.
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77
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78 * Improved region parsing. Colons in reference sequence names are parsed
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79 properly.
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80
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81 * Fixed an issue where mpileup does not apply BAQ for the first few reads when
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82 a region is specified.
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83
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84 * Fixed an issue where `faidx' does not work with FASTA files with long lines.
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85
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86 * Bugfix: wrong SP genotype information in the BCF output.
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87
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88 Other notable changes in bcftools:
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89
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90 * Output the ML esitmate of the allele count.
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91
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92 * Added the HWE plus F<0 filter to varFilter. For multiple samples, it
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93 effectively filters false heterozygous calls around centromeres.
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94
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95 * For association mapping, perform both 1-degree and 2-degree test. The
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96 2-degree test is conservative but more robust to HWE violation.
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97
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98 (0.1.17: 6 July 2011, r973:277)
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99
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100
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101
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102 Beta Release 0.1.16 (21 April, 2011)
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103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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104
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105 Notable changes in samtools:
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106
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107 * Support the new SAM/BAM type `B' in the latest SAM spec v1.4.
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108
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109 * When the output file of `samtools merge' exists, do not overwrite it unless
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110 a new command-line option `-f' is applied.
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111
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112 * Bugfix: BED support is not working when the input BED is not sorted.
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113
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114 * Bugfix: some reads without coordinates but given on the reverse strand are
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115 lost in merging.
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116
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117 Notable changes in bcftools:
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118
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119 * Code cleanup: separated max-likelihood inference and Bayesian inference.
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120
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121 * Test Hardy-Weinberg equilibrium with a likelihood-ratio test.
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122
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123 * Provided another association test P-value by likelihood-ratio test.
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124
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125 * Use Brent's method to estimate the site allele frequency when EM converges
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126 slowly. The resulting ML estimate of allele frequnecy is more accurate.
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127
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128 * Added the `ldpair' command, which computes r^2 between SNP pairs given in
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129 an input file.
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130
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131 Also, the `pileup' command, which has been deprecated by `mpileup' since
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132 version 0.1.10, will be dropped in the next release. The old `pileup' command
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133 is substandard and causing a lot of confusion.
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134
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135 (0.1.16: 21 April 2011, r963:234)
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136
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137
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138
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139 Beta Release 0.1.15 (10 April, 2011)
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140 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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141
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142 Noteable changes:
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143
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144 * Allow to perform variant calling or to extract information in multiple
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145 regions specified by a BED file (`samtools mpileup -l', `samtools view -L'
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146 and `bcftools view -l').
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147
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148 * Added the `depth' command to samtools to compute the per-base depth with a
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149 simpler interface. File `bam2depth.c', which implements this command, is the
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150 recommended example on how to use the mpileup APIs.
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151
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152 * Estimate genotype frequencies with ML; perform chi^2 based Hardy-Weinberg
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153 test using this estimate.
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154
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155 * For `samtools view', when `-R' is specified, drop read groups in the header
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156 that are not contained in the specified file.
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157
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158 * For `samtools flagstat', separate QC-pass and QC-fail reads.
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159
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160 * Improved the command line help of `samtools mpileup' and `bcftools view'.
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161
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162 * Use a global variable to control the verbose level of samtools stderr
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163 output. Nonetheless, it has not been full utilized.
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164
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165 * Fixed an issue in association test which may report false associations,
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166 possibly due to floating point underflow.
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167
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168 (0.1.15: 10 April 2011, r949:203)
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169
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170
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171
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172 Beta release 0.1.14 (21 March, 2011)
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173 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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174
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175 This release implements a method for testing associations for case-control
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176 data. The method does not call genotypes but instead sums over all genotype
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177 configurations to compute a chi^2 based test statistics. It can be potentially
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178 applied to comparing a pair of samples (e.g. a tumor-normal pair), but this
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179 has not been evaluated on real data.
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180
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181 Another new feature is to make X chromosome variant calls when female and male
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182 samples are both present. The user needs to provide a file indicating the
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183 ploidy of each sample (see also manual bcftools/bcftools.1).
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184
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185 Other notable changes:
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186
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187 * Added `bcftools view -F' to parse BCF files generated by samtools r921 or
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188 older which encodes PL in a different way.
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189
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190 * Changed the behavior of `bcftools view -s'. Now when a list of samples is
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191 provided, the samples in the output will be reordered to match the ordering
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192 in the sample list. This change is mainly designed for association test.
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193
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194 * Sped up `bcftools view -v' for target sequencing given thousands of samples.
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195 Also added a new option `view -d' to skip loci where only a few samples are
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196 covered by reads.
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197
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198 * Dropped HWE test. This feature has never been implemented properly. An EM
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199 should be much better. To be implemented in future.
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200
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201 * Added the `cat' command to samtools. This command concatenate BAMs with
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202 identical sequence dictionaries in an efficient way. Modified from bam_cat.c
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203 written by Chris Saunders.
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204
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205 * Added `samtools view -1' to write BAMs at a low compression level but twice
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206 faster to create. The `sort' command generates temporary files at a low
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207 compression level as well.
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208
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209 * Added `samtools mpileup -6' to accept "BAM" with Illumina 1.3+ quality
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210 strings (strictly speaking, such a file is not BAM).
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211
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212 * Added `samtools mpileup -L' to skip INDEL calling in regions with
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213 excessively high coverage. Such regions dramatically slow down mpileup.
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214
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215 * Updated `misc/export2sam.pl', provided by Chris Saunders from Illumina Inc.
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216
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217 (0.1.14: 21 March 2011, r933:170)
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218
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219
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220
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221 Beta release 0.1.13 (1 March, 2011)
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222 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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223
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224 The most important though largely invisible modification is the change of the
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225 order of genotypes in the PL VCF/BCF tag. This is to conform the upcoming VCF
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226 spec v4.1. The change means that 0.1.13 is not backward compatible with VCF/BCF
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227 generated by samtools older than r921 inclusive. VCF/BCF generated by the new
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228 samtools will contain a line `##fileformat=VCFv4.1' as well as the samtools
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229 version number.
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230
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231 Single Individual Haplotyping (SIH) is added as an experimental feature. It
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232 originally aims to produce haploid consensus from fosmid pool sequencing, but
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233 also works with short-read data. For short reads, phased blocks are usually too
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234 short to be useful in many applications, but they can help to rule out part of
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235 SNPs close to INDELs or between copies of CNVs.
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236
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237
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238 Other notable changes in samtools:
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239
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240 * Construct per-sample consensus to reduce the effect of nearby SNPs in INDEL
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241 calling. This reduces the power but improves specificity.
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242
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243 * Improved sorting order checking in indexing. Now indexing is the preferred way
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244 to check if a BAM is sorted.
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245
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246 * Added a switch `-E' to mpileup and calmd. This option uses an alternative way
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247 to apply BAQ, which increases sensistivity, especially to MNPs, at the cost of
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248 a little loss in specificity.
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249
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250 * Added `mpileup -A' to allow to use reads in anomalous pairs in SNP calling.
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251
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252 * Added `mpileup -m' to allow fine control of the collection of INDEL candidates.
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253
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254 * Added `mpileup -S' to compute per-sample strand bias P-value.
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255
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256 * Added `mpileup -G' to exclude read groups in variant calling.
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257
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258 * Fixed segfault in indel calling related to unmapped and refskip reads.
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259
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260 * Fixed an integer overflow in INDEL calling. This bug produces wrong INDEL
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261 genotypes for longer short INDELs, typically over 10bp.
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262
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263 * Fixed a bug in tview on big-endian machines.
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264
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265 * Fixed a very rare memory issue in bam_md.c
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266
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267 * Fixed an out-of-boundary bug in mpileup when the read base is `N'.
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268
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269 * Fixed a compiling error when the knetfile library is not used. Fixed a
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270 library compiling error due to the lack of bam_nt16_nt4_table[] table.
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271 Suppress a compiling warning related to the latest zlib.
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272
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273
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274 Other notable changes in bcftools:
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275
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276 * Updated the BCF spec.
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277
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278 * Added the `FQ' VCF INFO field, which gives the phred-scaled probability
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279 of all samples being the same (identical to the reference or all homozygous
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280 variants). Option `view -f' has been dropped.
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281
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282 * Implementated of "vcfutils.pl vcf2fq" to generate a consensus sequence
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283 similar to "samtools.pl pileup2fq".
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284
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285 * Make sure the GT FORMAT field is always the first FORMAT to conform the VCF
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286 spec. Drop bcf-fix.pl.
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287
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288 * Output bcftools specific INFO and FORMAT in the VCF header.
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289
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290 * Added `view -s' to call variants from a subset of samples.
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291
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292 * Properly convert VCF to BCF with a user provided sequence dictionary. Nonetheless,
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293 custom fields are still unparsed and will be stored as a missing value.
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294
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295 * Fixed a minor bug in Fisher's exact test; the results are rarely changed.
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296
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297
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298 (0.1.13: 1 March 2011, r926:134)
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299
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300
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301
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302 Beta release 0.1.12a (2 December, 2010)
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303 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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304
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305 This is another bug fix release:
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306
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307 * Fixed a memory violation in mpileup, which causes segfault. Release
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308 0.1.9 and above are affected.
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309
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310 * Fixed a memory violation in the indel caller, which does not causes
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311 segfault, but may potentially affect deletion calls in an unexpected
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312 way. Release 0.1.10 and above are affected.
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313
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314 * Fixed a bug in computing r-square in bcftools. Few are using this
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315 functionality and it only has minor effect.
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316
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317 * Fixed a memory leak in bam_fetch().
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318
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319 * Fixed a bug in writing meta information to the BAM index for the last
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320 sequence. This bug is invisible to most users, but it is a bug anyway.
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321
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322 * Fixed a bug in bcftools which causes false "DP4=0,0,0,0" annotations.
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323
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324 (0.1.12: 2 December 2010, r862)
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325
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326
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327
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328 Beta release 0.1.11 (21 November, 2010)
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329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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330
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331 This is mainly a bug fix release:
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332
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333 * Fixed a bug in random retrieval (since 0.1.8). It occurs when reads
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334 are retrieved from a small region containing no reads.
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335
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336 * Fixed a bug in pileup (since 0.1.9). The bug causes an assertion
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337 failure when the first CIGAR operation is a deletion.
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338
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339 * Improved fault tolerence in remote access.
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340
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341 One minor feature has been implemented in bcftools:
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342
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343 * Added a reference-free variant calling mode. In this mode, a site is
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344 regarded as a variat iff the sample(s) contains two or more alleles;
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345 the meaning of the QUAL field in the VCF output is changed
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346 accordingly. Effectively, the reference allele is irrelevant to the
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347 result in the new mode, although the reference sequence has to be
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348 used in realignment when SAMtools computes genotype likelihoods.
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349
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350 In addition, since 0.1.10, the `pileup' command has been deprecated by
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351 `mpileup' which is more powerful and more accurate. The `pileup' command
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352 will not be removed in the next few releases, but new features will not
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353 be added.
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354
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355 (0.1.11: 21 November 2010, r851)
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356
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357
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358
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359 Beta Release 0.1.10 (16 November, 2010)
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360 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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361
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362 This release is featured as the first major improvement to the indel
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363 caller. The method is similar to the old one implemented in the pileup
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364 command, but the details are handled more carefully both in theory and
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365 in practice. As a result, the new indel caller usually gives more
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366 accurate indel calls, though at the cost of sensitivity. The caller is
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367 implemented in the mpileup command and is invoked by default. It works
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368 with multiple samples.
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369
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370 Other notable changes:
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371
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372 * With the -r option, the calmd command writes the difference between
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373 the original base quality and the BAQ capped base quality at the BQ
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374 tag but does not modify the base quality. Please use -Ar to overwrite
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375 the original base quality (the 0.1.9 behavior).
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376
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377 * Allow to set a maximum per-sample read depth to reduce memory. In
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378 0.1.9, most of memory is wasted for the ultra high read depth in some
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379 regions (e.g. the chr1 centromere).
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380
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381 * Optionally write per-sample read depth and per-sample strand bias
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382 P-value.
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383
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384 * Compute equal-tail (Bayesian) credible interval of site allele
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385 frequency at the CI95 VCF annotation.
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386
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387 * Merged the vcfutils.pl varFilter and filter4vcf for better SNP/indel
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388 filtering.
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389
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390 (0.1.10: 16 November 2010, r829)
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391
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392
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393
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394 Beta Release 0.1.9 (27 October, 2010)
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395 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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396
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397 This release is featured as the first major improvement to the samtools'
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398 SNP caller. It comes with a revised MAQ error model, the support of
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399 multi-sample SNP calling and the computation of base alignment quality
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400 (BAQ).
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401
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402 The revised MAQ error model is based on the original model. It solves an
|
|
|
403 issue of miscalling SNPs in repetitive regions. Althought such SNPs can
|
|
|
404 usually be filtered at a later step, they mess up unfiltered calls. This
|
|
|
405 is a theoretical flaw in the original model. The revised MAQ model
|
|
|
406 deprecates the orginal MAQ model and the simplified SOAPsnp model.
|
|
|
407
|
|
|
408 Multi-sample SNP calling is separated in two steps. The first is done by
|
|
|
409 samtools mpileup and the second by a new program, bcftools, which is
|
|
|
410 included in the samtools source code tree. Multi-sample SNP calling also
|
|
|
411 works for single sample and has the advantage of enabling more powerful
|
|
|
412 filtration. It is likely to deprecate pileup in future once a proper
|
|
|
413 indel calling method is implemented.
|
|
|
414
|
|
|
415 BAQ is the Phred-scaled probability of a read base being wrongly
|
|
|
416 aligned. Capping base quality by BAQ has been shown to be very effective
|
|
|
417 in suppressing false SNPs caused by misalignments around indels or in
|
|
|
418 low-complexity regions with acceptable compromise on computation
|
|
|
419 time. This strategy is highly recommended and can be used with other SNP
|
|
|
420 callers as well.
|
|
|
421
|
|
|
422 In addition to the three major improvements, other notable changes are:
|
|
|
423
|
|
|
424 * Changes to the pileup format. A reference skip (the N CIGAR operator)
|
|
|
425 is shown as '<' or '>' depending on the strand. Tview is also changed
|
|
|
426 accordingly.
|
|
|
427
|
|
|
428 * Accelerated pileup. The plain pileup is about 50% faster.
|
|
|
429
|
|
|
430 * Regional merge. The merge command now accepts a new option to merge
|
|
|
431 files in a specified region.
|
|
|
432
|
|
|
433 * Fixed a bug in bgzip and razip which causes source files to be
|
|
|
434 deleted even if option -c is applied.
|
|
|
435
|
|
|
436 * In APIs, propogate errors to downstream callers and make samtools
|
|
|
437 return non-zero values once errors occur.
|
|
|
438
|
|
|
439 (0.1.9: 27 October 2010, r783)
|
|
|
440
|
|
|
441
|
|
|
442
|
|
|
443 Beta Release 0.1.8 (11 July, 2010)
|
|
|
444 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
445
|
|
|
446 Notable functional changes:
|
|
|
447
|
|
|
448 * Added the `reheader' command which replaces a BAM header with a new
|
|
|
449 header. This command is much faster than replacing header by
|
|
|
450 BAM->SAM->BAM conversions.
|
|
|
451
|
|
|
452 * Added the `mpileup' command which computes the pileup of multiple
|
|
|
453 alignments.
|
|
|
454
|
|
|
455 * The `index' command now stores the number of mapped and unmapped
|
|
|
456 reads in the index file. This information can be retrieved quickly by
|
|
|
457 the new `idxstats' command.
|
|
|
458
|
|
|
459 * By default, pileup used the SOAPsnp model for SNP calling. This
|
|
|
460 avoids the floating overflow in the MAQ model which leads to spurious
|
|
|
461 calls in repetitive regions, although these calls will be immediately
|
|
|
462 filtered by varFilter.
|
|
|
463
|
|
|
464 * The `tview' command now correctly handles CIGARs like 7I10M and
|
|
|
465 10M1P1I10M which cause assertion failure in earlier versions.
|
|
|
466
|
|
|
467 * Tview accepts a region like `=10,000' where `=' stands for the
|
|
|
468 current sequence name. This saves typing for long sequence names.
|
|
|
469
|
|
|
470 * Added the `-d' option to `pileup' which avoids slow indel calling
|
|
|
471 in ultradeep regions by subsampling reads locally.
|
|
|
472
|
|
|
473 * Added the `-R' option to `view' which retrieves alignments in read
|
|
|
474 groups listed in the specified file.
|
|
|
475
|
|
|
476 Performance improvements:
|
|
|
477
|
|
|
478 * The BAM->SAM conversion is up to twice faster, depending on the
|
|
|
479 characteristic of the input.
|
|
|
480
|
|
|
481 * Parsing SAM headers with a lot of reference sequences is now much
|
|
|
482 faster.
|
|
|
483
|
|
|
484 * The number of lseek() calls per query is reduced when the query
|
|
|
485 region contains no read alignments.
|
|
|
486
|
|
|
487 Bug fixes:
|
|
|
488
|
|
|
489 * Fixed an issue in the indel caller that leads to miscall of indels.
|
|
|
490 Note that this solution may not work well when the sequencing indel
|
|
|
491 error rate is higher than the rate of SNPs.
|
|
|
492
|
|
|
493 * Fixed another issue in the indel caller which may lead to incorrect
|
|
|
494 genotype.
|
|
|
495
|
|
|
496 * Fixed a bug in `sort' when option `-o' is applied.
|
|
|
497
|
|
|
498 * Fixed a bug in `view -r'.
|
|
|
499
|
|
|
500 APIs and other changes:
|
|
|
501
|
|
|
502 * Added iterator interfaces to random access and pileup. The callback
|
|
|
503 interfaces directly call the iterator interfaces.
|
|
|
504
|
|
|
505 * The BGZF blocks holding the BAM header are indepedent of alignment
|
|
|
506 BGZF blocks. Alignment records shorter than 64kB is guaranteed to be
|
|
|
507 fully contained in one BGZF block. This change is fully compatible
|
|
|
508 with the old version of samtools/picard.
|
|
|
509
|
|
|
510 Changes in other utilities:
|
|
|
511
|
|
|
512 * Updated export2sam.pl by Chris Saunders.
|
|
|
513
|
|
|
514 * Improved the sam2vcf.pl script.
|
|
|
515
|
|
|
516 * Added a Python version of varfilter.py by Aylwyn Scally.
|
|
|
517
|
|
|
518 (0.1.8: 11 July 2010, r613)
|
|
|
519
|
|
|
520
|
|
|
521
|
|
|
522 Beta Release 0.1.7 (10 November, 2009)
|
|
|
523 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
524
|
|
|
525 Notable changes:
|
|
|
526
|
|
|
527 * Improved the indel caller in complex scenariors, in particular for
|
|
|
528 long reads. The indel caller is now able to make reasonable indel
|
|
|
529 calls from Craig Venter capillary reads.
|
|
|
530
|
|
|
531 * Rewrote single-end duplicate removal with improved
|
|
|
532 performance. Paired-end reads are not touched.
|
|
|
533
|
|
|
534 * Duplicate removal is now library aware. Samtools remove potential
|
|
|
535 PCR/optical dupliates inside a library rather than across libraries.
|
|
|
536
|
|
|
537 * SAM header is now fully parsed, although this functionality is not
|
|
|
538 used in merging and so on.
|
|
|
539
|
|
|
540 * In samtools merge, optionally take the input file name as RG-ID and
|
|
|
541 attach the RG tag to each alignment.
|
|
|
542
|
|
|
543 * Added FTP support in the RAZF library. RAZF-compressed reference
|
|
|
544 sequence can be retrieved remotely.
|
|
|
545
|
|
|
546 * Improved network support for Win32.
|
|
|
547
|
|
|
548 * Samtools sort and merge are now stable.
|
|
|
549
|
|
|
550 Changes in other utilities:
|
|
|
551
|
|
|
552 * Implemented sam2vcf.pl that converts the pileup format to the VCF
|
|
|
553 format.
|
|
|
554
|
|
|
555 * This release of samtools is known to work with the latest
|
|
|
556 Bio-Samtools Perl module.
|
|
|
557
|
|
|
558 (0.1.7: 10 November 2009, r510)
|
|
|
559
|
|
|
560
|
|
|
561
|
|
|
562 Beta Release 0.1.6 (2 September, 2009)
|
|
|
563 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
564
|
|
|
565 Notable changes:
|
|
|
566
|
|
|
567 * In tview, do not show a blank screen when no reads mapped to the
|
|
|
568 corresponding region.
|
|
|
569
|
|
|
570 * Implemented native HTTP support in the BGZF library. Samtools is now
|
|
|
571 able to directly open a BAM file on HTTP. HTTP proxy is also
|
|
|
572 supported via the "http_proxy" environmental variable.
|
|
|
573
|
|
|
574 * Samtools is now compitable with the MinGW (win32) compiler and the
|
|
|
575 PDCurses library.
|
|
|
576
|
|
|
577 * The calmd (or fillmd) command now calculates the NM tag and replaces
|
|
|
578 MD tags if they are wrong.
|
|
|
579
|
|
|
580 * The view command now recognizes and optionally prints FLAG in HEXs or
|
|
|
581 strings to make a SAM file more friendly to human eyes. This is a
|
|
|
582 samtools-C extension, not implemented in Picard for the time
|
|
|
583 being. Please type `samtools view -?' for more information.
|
|
|
584
|
|
|
585 * BAM files now have an end-of-file (EOF) marker to facilitate
|
|
|
586 truncation detection. A warning will be given if an on-disk BAM file
|
|
|
587 does not have this marker. The warning will be seen on BAM files
|
|
|
588 generated by an older version of samtools. It does NO harm.
|
|
|
589
|
|
|
590 * New key bindings in tview: `r' to show read names and `s' to show
|
|
|
591 reference skip (N operation) as deletions.
|
|
|
592
|
|
|
593 * Fixed a bug in `samtools merge -n'.
|
|
|
594
|
|
|
595 * Samtools merge now optionally copies the header of a user specified
|
|
|
596 SAM file to the resultant BAM output.
|
|
|
597
|
|
|
598 * Samtools pileup/tview works with a CIGAR with the first or the last
|
|
|
599 operation is an indel.
|
|
|
600
|
|
|
601 * Fixed a bug in bam_aux_get().
|
|
|
602
|
|
|
603
|
|
|
604 Changes in other utilies:
|
|
|
605
|
|
|
606 * Fixed wrong FLAG in maq2sam.
|
|
|
607
|
|
|
608
|
|
|
609 (0.1.6: 2 September 2009, r453)
|
|
|
610
|
|
|
611
|
|
|
612
|
|
|
613 Beta Release 0.1.5 (7 July, 2009)
|
|
|
614 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
615
|
|
|
616 Notable changes:
|
|
|
617
|
|
|
618 * Support opening a BAM alignment on FTP. Users can now use "tview" to
|
|
|
619 view alignments at the NCBI ftp site. Please read manual for more
|
|
|
620 information.
|
|
|
621
|
|
|
622 * In library, propagate errors rather than exit or complain assertion
|
|
|
623 failure.
|
|
|
624
|
|
|
625 * Simplified the building system and fixed compiling errors caused by
|
|
|
626 zlib<1.2.2.1.
|
|
|
627
|
|
|
628 * Fixed an issue about lost header information when a SAM is imported
|
|
|
629 with "view -t".
|
|
|
630
|
|
|
631 * Implemented "samtool.pl varFilter" which filters both SNPs and short
|
|
|
632 indels. This command replaces "indelFilter".
|
|
|
633
|
|
|
634 * Implemented "samtools.pl pileup2fq" to generate FASTQ consensus from
|
|
|
635 pileup output.
|
|
|
636
|
|
|
637 * In pileup, cap mapping quality at 60. This helps filtering when
|
|
|
638 different aligners are in use.
|
|
|
639
|
|
|
640 * In pileup, allow to output variant sites only.
|
|
|
641
|
|
|
642 * Made pileup generate correct calls in repetitive region. At the same
|
|
|
643 time, I am considering to implement a simplified model in SOAPsnp,
|
|
|
644 although this has not happened yet.
|
|
|
645
|
|
|
646 * In view, added '-u' option to output BAM without compression. This
|
|
|
647 option is preferred when the output is piped to other commands.
|
|
|
648
|
|
|
649 * In view, added '-l' and '-r' to get the alignments for one library or
|
|
|
650 read group. The "@RG" header lines are now partially parsed.
|
|
|
651
|
|
|
652 * Do not include command line utilities to libbam.a.
|
|
|
653
|
|
|
654 * Fixed memory leaks in pileup and bam_view1().
|
|
|
655
|
|
|
656 * Made faidx more tolerant to empty lines right before or after FASTA >
|
|
|
657 lines.
|
|
|
658
|
|
|
659
|
|
|
660 Changes in other utilities:
|
|
|
661
|
|
|
662 * Updated novo2sam.pl by Colin Hercus, the key developer of novoalign.
|
|
|
663
|
|
|
664
|
|
|
665 This release involves several modifications to the key code base which
|
|
|
666 may potentially introduce new bugs even though we have tried to minimize
|
|
|
667 this by testing on several examples. Please let us know if you catch
|
|
|
668 bugs.
|
|
|
669
|
|
|
670 (0.1.5: 7 July 2009, r373)
|
|
|
671
|
|
|
672
|
|
|
673
|
|
|
674 Beta Release 0.1.4 (21 May, 2009)
|
|
|
675 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
676
|
|
|
677 Notable changes:
|
|
|
678
|
|
|
679 * Added the 'rmdupse' command: removing duplicates for SE reads.
|
|
|
680
|
|
|
681 * Fixed a critical bug in the indel caller: clipped alignments are not
|
|
|
682 processed correctly.
|
|
|
683
|
|
|
684 * Fixed a bug in the tview: gapped alignment may be incorrectly
|
|
|
685 displayed.
|
|
|
686
|
|
|
687 * Unified the interface to BAM and SAM I/O. This is done by
|
|
|
688 implementing a wrapper on top of the old APIs and therefore old APIs
|
|
|
689 are still valid. The new I/O APIs also recognize the @SQ header
|
|
|
690 lines.
|
|
|
691
|
|
|
692 * Generate the MD tag.
|
|
|
693
|
|
|
694 * Generate "=" bases. However, the indel caller will not work when "="
|
|
|
695 bases are present.
|
|
|
696
|
|
|
697 * Enhanced support of color-read display (by Nils Homer).
|
|
|
698
|
|
|
699 * Implemented the GNU building system. However, currently the building
|
|
|
700 system does not generate libbam.a. We will improve this later. For
|
|
|
701 the time being, `make -f Makefile.generic' is preferred.
|
|
|
702
|
|
|
703 * Fixed a minor bug in pileup: the first read in a chromosome may be
|
|
|
704 skipped.
|
|
|
705
|
|
|
706 * Fixed bugs in bam_aux.c. These bugs do not affect other components as
|
|
|
707 they were not used previously.
|
|
|
708
|
|
|
709 * Output the 'SM' tag from maq2sam.
|
|
|
710
|
|
|
711 (0.1.4: 21 May 2009, r297)
|
|
|
712
|
|
|
713
|
|
|
714
|
|
|
715 Beta Release 0.1.3 (15 April, 2009)
|
|
|
716 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
717
|
|
|
718 Notable changes in SAMtools:
|
|
|
719
|
|
|
720 * SAMtools is more consistent with the specification: a) '*' in the
|
|
|
721 QUAL field is allowed; b) the field separator is TAB only and SPACE
|
|
|
722 is treated as a character in a field; c) empty header is allowed.
|
|
|
723
|
|
|
724 * Implemented GLFv3 support in pileup.
|
|
|
725
|
|
|
726 * Fixed a severe bug in fixmate: strand information is wrongly
|
|
|
727 overwritten.
|
|
|
728
|
|
|
729 * Fixed a bug in alignment retrieval: alignments bridging n*16384bp are
|
|
|
730 not correctly retrieved sometimes.
|
|
|
731
|
|
|
732 * Fixed a bug in rmdup: segfault if unmapped reads are present.
|
|
|
733
|
|
|
734 * Move indel_filter.pl to samtools.pl and improved the filtering by
|
|
|
735 checking the actual number of alignments containing indels. The indel
|
|
|
736 pileup line is also changed a little to make this filtration easier.
|
|
|
737
|
|
|
738 * Fixed a minor bug in indexing: the bin number of an unmapped read is
|
|
|
739 wrongly calculated.
|
|
|
740
|
|
|
741 * Added `flagstat' command to show statistics on the FLAG field.
|
|
|
742
|
|
|
743 * Improved indel caller by setting the maximum window size in local
|
|
|
744 realignment.
|
|
|
745
|
|
|
746 Changes in other utilities:
|
|
|
747
|
|
|
748 * Fixed a bug in maq2sam: a tag name is obsolete.
|
|
|
749
|
|
|
750 * Improvement to wgsim: a) added support for SOLiD read simulation; b)
|
|
|
751 show the number of substitutions/indels/errors in read name; c)
|
|
|
752 considerable code clean up.
|
|
|
753
|
|
|
754 * Various converters: improved functionality in general.
|
|
|
755
|
|
|
756 * Updated the example SAM due to the previous bug in fixmate.
|
|
|
757
|
|
|
758 (0.1.3: 15 April 2009, r227)
|
|
|
759
|
|
|
760
|
|
|
761
|
|
|
762 Beta Release 0.1.2 (28 January, 2008)
|
|
|
763 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
764
|
|
|
765 Notable changes in SAMtools:
|
|
|
766
|
|
|
767 * Implemented a Bayesian indel caller. The new caller generate scores
|
|
|
768 and genotype and is potentially more accurate than Maq's indel
|
|
|
769 caller. The pileup format is also changed accordingly.
|
|
|
770
|
|
|
771 * Implemented rmdup command: remove potential PCR duplicates. Note that
|
|
|
772 this command ONLY works for FR orientation and requires ISIZE is
|
|
|
773 correctly set.
|
|
|
774
|
|
|
775 * Added fixmate command: fill in mate coordinates, ISIZE and mate
|
|
|
776 related flags from a name-sorted alignment.
|
|
|
777
|
|
|
778 * Fixed a bug in indexing: reads bridging 16x kbp were not retrieved.
|
|
|
779
|
|
|
780 * Allow to select reads shown in the pileup output with a mask.
|
|
|
781
|
|
|
782 * Generate GLFv2 from pileup.
|
|
|
783
|
|
|
784 * Added two more flags for flagging PCR/optical duplicates and for QC
|
|
|
785 failure.
|
|
|
786
|
|
|
787 * Fixed a bug in sort command: name sorting for large alignment did not
|
|
|
788 work.
|
|
|
789
|
|
|
790 * Allow to completely disable RAZF (using Makefile.lite) as some people
|
|
|
791 have problem to compile it.
|
|
|
792
|
|
|
793 * Fixed a bug in import command when there are reads without
|
|
|
794 coordinates.
|
|
|
795
|
|
|
796 * Fixed a bug in tview: clipping broke the alignment viewer.
|
|
|
797
|
|
|
798 * Fixed a compiling error when _NO_CURSES is applied.
|
|
|
799
|
|
|
800 * Fixed a bug in merge command.
|
|
|
801
|
|
|
802 Changes in other utilities:
|
|
|
803
|
|
|
804 * Added wgsim, a paired-end reads simulator. Wgsim was adapted from
|
|
|
805 maq's reads simulator. Colin Hercus further improved it to allow
|
|
|
806 longer indels.
|
|
|
807
|
|
|
808 * Added wgsim_eval.pl, a script that evaluates the accuracy of
|
|
|
809 alignment on reads generated by wgsim.
|
|
|
810
|
|
|
811 * Added soap2sam.pl, a SOAP2->SAM converter. This converter does not
|
|
|
812 work properly when multiple hits are output.
|
|
|
813
|
|
|
814 * Added bowtie2sam.pl, a Bowtie->SAM converter. Only the top hit will
|
|
|
815 be retained when multiple hits are present.
|
|
|
816
|
|
|
817 * Fixed a bug in export2sam.pl for QC reads.
|
|
|
818
|
|
|
819 * Support RG tag at MAQ->SAM converter.
|
|
|
820
|
|
|
821 * Added novo2sam.pl, a NovoAlign->SAM converter. Multiple hits and
|
|
|
822 indel are not properly handled, though.
|
|
|
823
|
|
|
824 * Added zoom2sam.pl, a ZOOM->SAM converter. It only works with the
|
|
|
825 default Illumina output.
|
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|
826
|
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|
827 (0.1.2: 28 January 2008; r116)
|
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|
828
|
|
|
829
|
|
|
830
|
|
|
831 Beta Release 0.1.1 (22 December, 2008)
|
|
|
832 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
833
|
|
|
834 The is the first public release of samtools. For more information,
|
|
|
835 please check the manual page `samtools.1' and the samtools website
|
|
|
836 http://samtools.sourceforge.net
|
