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1 Release 0.7.9 (19 May, 2014)
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2 ----------------------------
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3
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4 This release brings several major changes to BWA-MEM. Notably, BWA-MEM now
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5 formally supports PacBio read-to-reference alignment and experimentally supports
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6 PacBio read-to-read alignment. BWA-MEM also runs faster at a minor cost of
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7 accuracy. The speedup is more significant when GRCh38 is in use. More
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8 specifically:
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9
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10 * Support PacBio subread-to-reference alignment. Although older BWA-MEM works
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11 with PacBio data in principle, the resultant alignments are frequently
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12 fragmented. In this release, we fine tuned existing methods and introduced
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13 new heuristics to improve PacBio alignment. These changes are not used by
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14 default. Users need to add option "-x pacbio" to enable the feature.
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15
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16 * Support PacBio subread-to-subread alignment (EXPERIMENTAL). This feature is
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17 enabled with option "-x pbread". In this mode, the output only gives the
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18 overlapping region between a pair of reads without detailed alignment.
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19
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20 * Output alternative hits in the XA tag if there are not so many of them. This
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21 is a BWA-backtrack feature.
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22
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23 * Support mapping to ALT contigs in GRCh38 (EXPERIMENTAL). We provide a script
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24 to postprocess hits in the XA tag to adjust the mapping quality and generate
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25 new primary alignments to all overlapping ALT contigs. We would *NOT*
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26 recommend this feature for production uses.
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27
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28 * Improved alignments to many short reference sequences. Older BWA-MEM may
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29 generate an alignment bridging two or more adjacent reference sequences.
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30 Such alignments are split at a later step as postprocessing. This approach
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31 is complex and does not always work. This release forbids these alignments
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32 from the very beginning. BWA-MEM should not produce an alignment bridging
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33 two or more reference sequences any more.
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34
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35 * Reduced the maximum seed occurrence from 10000 to 500. Reduced the maximum
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36 rounds of Smith-Waterman mate rescue from 100 to 50. Added a heuristic to
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37 lower the mapping quality if a read contains seeds with excessive
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38 occurrences. These changes make BWA-MEM faster at a minor cost of accuracy
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39 in highly repetitive regions.
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40
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41 * Added an option "-Y" to use soft clipping for supplementary alignments.
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42
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43 * Bugfix: incomplete alignment extension in corner cases.
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44
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45 * Bugfix: integer overflow when aligning long query sequences.
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46
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47 * Bugfix: chain score is not computed correctly (almost no practical effect)
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48
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49 * General code cleanup
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50
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51 * Added FAQs to README
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52
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53 Changes in BWA-backtrack:
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54
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55 * Bugfix: a segmentation fault when an alignment stands out of the end of the
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56 last chromosome.
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57
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58 (0.7.9: 19 May 2014, r783)
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59
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60
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61
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62 Release 0.7.8 (31 March, 2014)
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63 ------------------------------
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64
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65 Changes in BWA-MEM:
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66
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67 * Bugfix: off-diagonal X-dropoff (option -d) not working as intended.
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68 Short-read alignment is not affected.
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69
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70 * Bugfix: unnecessarily large bandwidth used during global alignment,
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71 which reduces the mapping speed by -5% for short reads. Results are not
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72 affected.
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73
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74 * Bugfix: when the matching score is not one, paired-end mapping quality is
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75 inaccurate.
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76
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77 * When the matching score (option -A) is changed, scale all score-related
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78 options accordingly unless overridden by users.
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79
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80 * Allow to specify different gap open (or extension) penalties for deletions
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81 and insertions separately.
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82
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83 * Allow to specify the insert size distribution.
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84
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85 * Better and more detailed debugging information.
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86
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87 With the default setting, 0.7.8 and 0.7.7 gave identical output on one million
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88 100bp read pairs.
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89
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90 (0.7.8: 31 March 2014, r455)
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91
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92
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93
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94 Release 0.7.7 (25 Feburary, 2014)
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95 ---------------------------------
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96
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97 This release fixes incorrect MD tags in the BWA-MEM output.
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98
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99 A note about short-read mapping to GRCh38. The new human reference genome
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100 GRCh38 contains 60Mbp program generated alpha repeat arrays, some of which are
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101 hard masked as they cannot be localized. These highly repetitive arrays make
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102 BWA-MEM -50% slower. If you are concerned with the performance of BWA-MEM, you
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103 may consider to use option "-c2000 -m50". On simulated data, this setting helps
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104 the performance at a very minor cost on accuracy. I may consider to change the
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105 default in future releases.
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106
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107 (0.7.7: 25 Feburary 2014, r441)
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108
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109
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110
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111 Release 0.7.6 (31 Januaray, 2014)
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112 ---------------------------------
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113
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114 Changes in BWA-MEM:
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115
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116 * Changed the way mapping quality is estimated. The new method tends to give
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117 the same alignment a higher mapping quality. On paired-end reads, the change
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118 is minor as with pairing, the mapping quality is usually high. For short
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119 single-end reads, the difference is considerable.
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120
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121 * Improved load balance when many threads are spawned. However, bwa-mem is
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122 still not very thread efficient, probably due to the frequent heap memory
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123 allocation. Further improvement is a little difficult and may affect the
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124 code stability.
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125
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126 * Allow to use different clipping penalties for 5'- and 3'-ends. This helps
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127 when we do not want to clip one end.
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128
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129 * Print the @PG line, including the command line options.
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130
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131 * Improved the band width estimate: a) fixed a bug causing the band
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132 width extimated from extension not used in the final global alignment; b)
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133 try doubled band width if the global alignment score is smaller.
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134 Insufficient band width leads to wrong CIGAR and spurious mismatches/indels.
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135
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136 * Added a new option -D to fine tune a heuristic on dropping suboptimal hits.
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137 Reducing -D increases accuracy but decreases the mapping speed. If unsure,
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138 leave it to the default.
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139
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140 * Bugfix: for a repetitive single-end read, the reported hit is not randomly
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141 distributed among equally best hits.
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142
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143 * Bugfix: missing paired-end hits due to unsorted list of SE hits.
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144
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145 * Bugfix: incorrect CIGAR caused by a defect in the global alignment.
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146
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147 * Bugfix: incorrect CIGAR caused by failed SW rescue.
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148
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149 * Bugfix: alignments largely mapped to the same position are regarded to be
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150 distinct from each other, which leads to underestimated mapping quality.
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151
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152 * Added the MD tag.
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153
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154 There are no changes to BWA-backtrack in this release. However, it has a few
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155 known issues yet to be fixed. If you prefer BWA-track, It is still advised to
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156 use bwa-0.6.x.
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157
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158 While I developed BWA-MEM, I also found a few issues with BWA-SW. It is now
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159 possible to improve BWA-SW with the lessons learned from BWA-MEM. However, as
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160 BWA-MEM is usually better, I will not improve BWA-SW until I find applications
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161 where BWA-SW may excel.
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162
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163 (0.7.6: 31 January 2014, r432)
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164
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165
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166
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167 Release 0.7.5a (30 May, 2013)
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168 -----------------------------
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169
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170 Fixed a bug in BWA-backtrack which leads to off-by-one mapping errors in rare
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171 cases.
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172
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173 (0.7.5a: 30 May 2013, r405)
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174
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175
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176
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177 Release 0.7.5 (29 May, 2013)
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178 ----------------------------
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179
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180 Changes in all components:
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181
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182 * Improved error checking on memory allocation and file I/O. Patches provided
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183 by Rob Davies.
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184
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185 * Updated README.
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186
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187 * Bugfix: return code is zero upon errors.
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188
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189 Changes in BWA-MEM:
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190
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191 * Changed the way a chimeric alignment is reported (conforming to the upcoming
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192 SAM spec v1.5). With 0.7.5, if the read has a chimeric alignment, the paired
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193 or the top hit uses soft clipping and is marked with neither 0x800 nor 0x100
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194 bits. All the other hits part of the chimeric alignment will use hard
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195 clipping and be marked with 0x800 if option "-M" is not in use, or marked
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196 with 0x100 otherwise.
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197
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198 * Other hits part of a chimeric alignment are now reported in the SA tag,
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199 conforming to the SAM spec v1.5.
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200
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201 * Better method for resolving an alignment bridging two or more short
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202 reference sequences. The current strategy maps the query to the reference
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203 sequence that covers the middle point of the alignment. For most
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204 applications, this change has no effects.
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205
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206 Changes in BWA-backtrack:
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207
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208 * Added a magic number to .sai files. This prevents samse/sampe from reading
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209 corrupted .sai (e.g. a .sai file containing LSF log) or incompatible .sai
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210 generated by a different version of bwa.
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211
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212 * Bugfix: alignments in the XA:Z: tag were wrong.
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213
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214 * Keep track of #ins and #del during backtracking. This simplifies the code
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215 and reduces errors in rare corner cases. I should have done this in the
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216 early days of bwa.
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217
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218 In addition, if you use BWA-MEM or the fastmap command of BWA, please cite:
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219
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220 - Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs
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221 with BWA-MEM. arXiv:1303.3997v2 [q-bio.GN].
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222
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223 Thank you.
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224
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225 (0.7.5: 29 May 2013, r404)
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226
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227
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228
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229 Release 0.7.4 (23 April, 2013)
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230 ------------------------------
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231
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232 This is a bugfix release. Most of bugs are considered to be minor which only
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233 occur very rarely.
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234
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235 * Bugfix: wrong CIGAR when a query sequence bridges three or more target
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236 sequences. This only happens when aligning reads to short assembly contigs.
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237
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238 * Bugfix: leading "D" operator in CIGAR.
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239
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240 * Extend more seeds for better alignment around tandem repeats. This is also
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241 a cause of the leading "D" operator in CIGAR.
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242
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243 * Bugfix: SSE2-SSW may occasionally find incorrect query starting position
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244 around tandem repeat. This will lead to a suboptimal CIGAR in BWA-MEM and
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245 a wrong CIGAR in BWA.
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246
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247 * Bugfix: clipping penalty does not work as is intended when there is a gap
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248 towards the end of a read.
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249
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250 * Fixed an issue caused by a bug in the libc from Mac/Darwin. In Darwin,
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251 fread() is unable to read a data block longer than 2GB due to an integer
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252 overflow bug in its implementation.
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253
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254 Since version 0.7.4, BWA-MEM is considered to reach similar stability to
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255 BWA-backtrack for short-read mapping.
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256
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257 (0.7.4: 23 April, r385)
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258
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259
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260
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261 Release 0.7.3a (15 March, 2013)
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262 -------------------------------
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263
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264 In 0.7.3, the wrong CIGAR bug was only fixed in one scenario, but not fixed
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265 in another corner case.
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266
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267 (0.7.3a: 15 March 2013, r367)
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268
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269
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270
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271 Release 0.7.3 (15 March, 2013)
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272 ------------------------------
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273
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274 Changes to BWA-MEM:
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275
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276 * Bugfix: pairing score is inaccurate when option -A does not take the default
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277 value. This is a very minor issue even if it happens.
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278
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279 * Bugfix: occasionally wrong CIGAR. This happens when in the alignment there
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280 is a 1bp deletion and a 1bp insertion which are close to the end of the
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281 reads, and there are no other substitutions or indels. BWA-MEM would not do
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282 a gapped alignment due to the bug.
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283
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284 * New feature: output other non-overlapping alignments in the XP tag such that
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285 we can see the entire picture of alignment from one SAM line. XP gives the
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286 position, CIGAR, NM and mapQ of each aligned subsequence of the query.
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287
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288 BWA-MEM has been used to align -300Gbp 100-700bp SE/PE reads. SNP/indel calling
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289 has also been evaluated on part of these data. BWA-MEM generally gives better
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290 pre-filtered SNP calls than BWA. No significant issues have been observed since
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291 0.7.2, though minor improvements or bugs (e.g. the bug fixed in this release)
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292 are still possible. If you find potential issues, please send bug reports to
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293 <bio-bwa-help@lists.sourceforge.net> (free registration required).
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294
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295 In addition, more detailed description of the BWA-MEM algorithm can be found at
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296 <https://github.com/lh3/mem-paper>.
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297
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298 (0.7.3: 15 March 2013, r366)
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299
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300
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301
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302 Release 0.7.2 (9 March, 2013)
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303 -----------------------------
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304
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305 Emergent bug fix: 0.7.0 and 0.7.1 give a wrong sign to TLEN. In addition,
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306 flagging 'properly paired' also gets improved a little.
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307
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308 (0.7.2: 9 March 2013, r351)
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309
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310
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311
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312 Release 0.7.1 (8 March, 2013)
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313 -----------------------------
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314
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315 Changes to BWA-MEM:
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316
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317 * Bugfix: rare segmentation fault caused by a partial hit to the end of the
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318 last sequence.
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319
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320 * Bugfix: occasional mis-pairing given an interleaved fastq.
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321
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322 * Bugfix: wrong mate information when the mate is unmapped. SAM generated by
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323 BWA-MEM can now be validated with Picard.
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324
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325 * Improved the performance and accuracy for ultra-long query sequences.
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326 Short-read alignment is not affected.
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327
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328 Changes to other components:
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329
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330 * In BWA-backtrack and BWA-SW, replaced the code for global alignment,
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331 Smith-Waterman and SW extension. The performance and accuracy of the two
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332 algorithms stay the same.
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333
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334 * Added an experimental subcommand to merge overlapping paired ends. The
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335 algorithm is very conservative: it may miss true overlaps but rarely makes
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336 mistakes.
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337
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338 An important note is that like BWA-SW, BWA-MEM may output multiple primary
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339 alignments for a read, which may cause problems to some tools. For aligning
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340 sequence reads, it is advised to use '-M' to flag extra hits as secondary. This
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341 option is not the default because multiple primary alignments are theoretically
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342 possible in sequence alignment.
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343
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344 (0.7.1: 8 March 2013, r347)
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345
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346
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347
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348 Beta Release 0.7.0 (28 Feburary, 2013)
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349 --------------------------------------
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350
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351 This release comes with a new alignment algorithm, BWA-MEM, for 70bp-1Mbp query
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352 sequences. BWA-MEM essentially seeds alignments with a variant of the fastmap
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353 algorithm and extends seeds with banded affine-gap-penalty dynamic programming
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354 (i.e. the Smith-Waterman-Gotoh algorithm). For typical Illumina 100bp reads or
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355 longer low-divergence query sequences, BWA-MEM is about twice as fast as BWA
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356 and BWA-SW and is more accurate. It also supports split alignments like BWA-SW
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357 and may optionally output multiple hits like BWA. BWA-MEM does not guarantee
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358 to find hits within a certain edit distance, but BWA is not efficient for such
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359 task given longer reads anyway, and the edit-distance criterion is arguably
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360 not as important in long-read alignment.
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361
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362 In addition to the algorithmic improvements, BWA-MEM also implements a few
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363 handy features in practical aspects:
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364
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365 1. BWA-MEM automatically switches between local and glocal (global wrt reads;
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366 local wrt reference) alignment. It reports the end-to-end glocal alignment
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367 if the glocal alignment is not much worse than the optimal local alignment.
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368 Glocal alignment reduces reference bias.
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369
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370 2. BWA-MEM automatically infers pair orientation from a batch of single-end
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371 alignments. It allows more than one orientations if there are sufficient
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372 supporting reads. This feature has not been tested on reads from Illumina
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373 jumping library yet. (EXPERIMENTAL)
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374
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375 3. BWA-MEM optionally takes one interleaved fastq for paired-end mapping. It
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376 is possible to convert a name-sorted BAM to an interleaved fastq on the fly
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377 and feed the data stream to BWA-MEM for mapping.
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378
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379 4. BWA-MEM optionally copies FASTA/Q comments to the final SAM output, which
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380 helps to transfer individual read annotations to the output.
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381
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382 5. BWA-MEM supports more advanced piping. Users can now run:
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383 (bwa mem ref.fa '<bzcat r1.fq.bz2' '<bzcat r2.fq.bz2') to map bzip'd read
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384 files without replying on bash features.
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385
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386 6. BWA-MEM provides a few basic APIs for single-end mapping. The 'example.c'
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387 program in the source code directory implements a full single-end mapper in
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388 50 lines of code.
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389
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390 The BWA-MEM algorithm is in the beta phase. It is not advised to use BWA-MEM
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391 for production use yet. However, when the implementation becomes stable after a
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392 few release cycles, existing BWA users are recommended to migrate to BWA-MEM
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393 for 76bp or longer Illumina reads and long query sequences. The original BWA
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|
|
394 short-read algorithm will not deliver satisfactory results for 150bp+ Illumina
|
|
|
395 reads. Change of mappers will be necessary sooner or later.
|
|
|
396
|
|
|
397 (0.7.0 beta: 28 Feburary 2013, r313)
|
|
|
398
|
|
|
399
|
|
|
400
|
|
|
401 Release 0.6.2 (19 June, 2012)
|
|
|
402 -----------------------------
|
|
|
403
|
|
|
404 This is largely a bug-fix release. Notable changes in BWA-short and BWA-SW:
|
|
|
405
|
|
|
406 * Bugfix: BWA-SW may give bad alignments due to incorrect band width.
|
|
|
407
|
|
|
408 * Bugfix: A segmentation fault due to an out-of-boundary error. The fix is a
|
|
|
409 temporary solution. The real cause has not been identified.
|
|
|
410
|
|
|
411 * Attempt to read index from prefix.64.bwt, such that the 32-bit and 64-bit
|
|
|
412 index can coexist.
|
|
|
413
|
|
|
414 * Added options '-I' and '-S' to control BWA-SW pairing.
|
|
|
415
|
|
|
416 (0.6.2: 19 June 2012, r126)
|
|
|
417
|
|
|
418
|
|
|
419
|
|
|
420 Release 0.6.1 (28 November, 2011)
|
|
|
421 ---------------------------------
|
|
|
422
|
|
|
423 Notable changes to BWA-short:
|
|
|
424
|
|
|
425 * Bugfix: duplicated alternative hits in the XA tag.
|
|
|
426
|
|
|
427 * Bugfix: when trimming enabled, bwa-aln trims 1bp less.
|
|
|
428
|
|
|
429 * Disabled the color-space alignment. 0.6.x is not working with SOLiD reads at
|
|
|
430 present.
|
|
|
431
|
|
|
432 Notable changes to BWA-SW:
|
|
|
433
|
|
|
434 * Bugfix: segfault due to excessive ambiguous bases.
|
|
|
435
|
|
|
436 * Bugfix: incorrect mate position in the SE mode.
|
|
|
437
|
|
|
438 * Bugfix: rare segfault in the PE mode
|
|
|
439
|
|
|
440 * When macro _NO_SSE2 is in use, fall back to the standard Smith-Waterman
|
|
|
441 instead of SSE2-SW.
|
|
|
442
|
|
|
443 * Optionally mark split hits with lower alignment scores as secondary.
|
|
|
444
|
|
|
445 Changes to fastmap:
|
|
|
446
|
|
|
447 * Bugfix: infinite loop caused by ambiguous bases.
|
|
|
448
|
|
|
449 * Optionally output the query sequence.
|
|
|
450
|
|
|
451 (0.6.1: 28 November 2011, r104)
|
|
|
452
|
|
|
453
|
|
|
454
|
|
|
455 Release 0.5.10 and 0.6.0 (12 November, 2011)
|
|
|
456 --------------------------------------------
|
|
|
457
|
|
|
458 The 0.6.0 release comes with two major changes. Firstly, the index data
|
|
|
459 structure has been changed to support genomes longer than 4GB. The forward and
|
|
|
460 reverse backward genome is now integrated in one index. This change speeds up
|
|
|
461 BWA-short by about 20% and BWA-SW by 90% with the mapping acccuracy largely
|
|
|
462 unchanged. A tradeoff is BWA requires more memory, but this is the price almost
|
|
|
463 all mappers that index the genome have to pay.
|
|
|
464
|
|
|
465 Secondly, BWA-SW in 0.6.0 now works with paired-end data. It is more accurate
|
|
|
466 for highly unique reads and more robust to long indels and structural
|
|
|
467 variations. However, BWA-short still has edges for reads with many suboptimal
|
|
|
468 hits. It is yet to know which algorithm is the best for variant calling.
|
|
|
469
|
|
|
470 0.5.10 is a bugfix release only and is likely to be the last release in the 0.5
|
|
|
471 branch unless I find critical bugs in future.
|
|
|
472
|
|
|
473 Other notable changes:
|
|
|
474
|
|
|
475 * Added the 'fastmap' command that finds super-maximal exact matches. It does
|
|
|
476 not give the final alignment, but runs much faster. It can be a building
|
|
|
477 block for other alignment algorithms. [0.6.0 only]
|
|
|
478
|
|
|
479 * Output the timing information before BWA exits. This also tells users that
|
|
|
480 the task has been finished instead of being killed or aborted. [0.6.0 only]
|
|
|
481
|
|
|
482 * Sped up multi-threading when using many (>20) CPU cores.
|
|
|
483
|
|
|
484 * Check I/O error.
|
|
|
485
|
|
|
486 * Increased the maximum barcode length to 63bp.
|
|
|
487
|
|
|
488 * Automatically choose the indexing algorithm.
|
|
|
489
|
|
|
490 * Bugfix: very rare segfault due to an uninitialized variable. The bug also
|
|
|
491 affects the placement of suboptimal alignments. The effect is very minor.
|
|
|
492
|
|
|
493 This release involves quite a lot of tricky changes. Although it has been
|
|
|
494 tested on a few data sets, subtle bugs may be still hidden. It is *NOT*
|
|
|
495 recommended to use this release in a production pipeline. In future, however,
|
|
|
496 BWA-SW may be better when reads continue to go longer. I would encourage users
|
|
|
497 to try the 0.6 release. I would also like to hear the users' experience. Thank
|
|
|
498 you.
|
|
|
499
|
|
|
500 (0.6.0: 12 November 2011, r85)
|
|
|
501
|
|
|
502
|
|
|
503
|
|
|
504 Beta Release 0.5.9 (24 January, 2011)
|
|
|
505 -------------------------------------
|
|
|
506
|
|
|
507 Notable changes:
|
|
|
508
|
|
|
509 * Feature: barcode support via the '-B' option.
|
|
|
510
|
|
|
511 * Feature: Illumina 1.3+ read format support via the '-I' option.
|
|
|
512
|
|
|
513 * Bugfix: RG tags are not attached to unmapped reads.
|
|
|
514
|
|
|
515 * Bugfix: very rare bwasw mismappings
|
|
|
516
|
|
|
517 * Recommend options for PacBio reads in bwasw help message.
|
|
|
518
|
|
|
519
|
|
|
520 Also, since January 13, the BWA master repository has been moved to github:
|
|
|
521
|
|
|
522 https://github.com/lh3/bwa
|
|
|
523
|
|
|
524 The revision number has been reset. All recent changes will be first
|
|
|
525 committed to this repository.
|
|
|
526
|
|
|
527 (0.5.9: 24 January 2011, r16)
|
|
|
528
|
|
|
529
|
|
|
530
|
|
|
531 Beta Release Candidate 0.5.9rc1 (10 December, 2010)
|
|
|
532 ---------------------------------------------------
|
|
|
533
|
|
|
534 Notable changes in bwasw:
|
|
|
535
|
|
|
536 * Output unmapped reads.
|
|
|
537
|
|
|
538 * For a repetitive read, choose a random hit instead of a fixed
|
|
|
539 one. This is not well tested.
|
|
|
540
|
|
|
541 Notable changes in bwa-short:
|
|
|
542
|
|
|
543 * Fixed a bug in the SW scoring system, which may lead to unexpected
|
|
|
544 gaps towards the end of a read.
|
|
|
545
|
|
|
546 * Fixed a bug which invalidates the randomness of repetitive reads.
|
|
|
547
|
|
|
548 * Fixed a rare memory leak.
|
|
|
549
|
|
|
550 * Allowed to specify the read group at the command line.
|
|
|
551
|
|
|
552 * Take name-grouped BAM files as input.
|
|
|
553
|
|
|
554 Changes to this release are usually safe in that they do not interfere
|
|
|
555 with the key functionality. However, the release has only been tested on
|
|
|
556 small samples instead of on large-scale real data. If anything weird
|
|
|
557 happens, please report the bugs to the bio-bwa-help mailing list.
|
|
|
558
|
|
|
559 (0.5.9rc1: 10 December 2010, r1561)
|
|
|
560
|
|
|
561
|
|
|
562
|
|
|
563 Beta Release 0.5.8 (8 June, 2010)
|
|
|
564 ---------------------------------
|
|
|
565
|
|
|
566 Notable changes in bwasw:
|
|
|
567
|
|
|
568 * Fixed an issue of missing alignments. This should happen rarely and
|
|
|
569 only when the contig/read alignment is multi-part. Very rarely, bwasw
|
|
|
570 may still miss a segment in a multi-part alignment. This is difficult
|
|
|
571 to fix, although possible.
|
|
|
572
|
|
|
573 Notable changes in bwa-short:
|
|
|
574
|
|
|
575 * Discard the SW alignment when the best single-end alignment is much
|
|
|
576 better. Such a SW alignment may caused by structural variations and
|
|
|
577 forcing it to be aligned leads to false alignment. This fix has not
|
|
|
578 been tested thoroughly. It would be great to receive more users
|
|
|
579 feedbacks on this issue.
|
|
|
580
|
|
|
581 * Fixed a typo/bug in sampe which leads to unnecessarily large memory
|
|
|
582 usage in some cases.
|
|
|
583
|
|
|
584 * Further reduced the chance of reporting 'weird pairing'.
|
|
|
585
|
|
|
586 (0.5.8: 8 June 2010, r1442)
|
|
|
587
|
|
|
588
|
|
|
589
|
|
|
590 Beta Release 0.5.7 (1 March, 2010)
|
|
|
591 ----------------------------------
|
|
|
592
|
|
|
593 This release only has an effect on paired-end data with fat insert-size
|
|
|
594 distribution. Users are still recommended to update as the new release
|
|
|
595 improves the robustness to poor data.
|
|
|
596
|
|
|
597 * The fix for 'weird pairing' was not working in version 0.5.6, pointed
|
|
|
598 out by Carol Scott. It should work now.
|
|
|
599
|
|
|
600 * Optionally output to a normal file rather than to stdout (by Tim
|
|
|
601 Fennel).
|
|
|
602
|
|
|
603 (0.5.7: 1 March 2010, r1310)
|
|
|
604
|
|
|
605
|
|
|
606
|
|
|
607 Beta Release 0.5.6 (10 Feburary, 2010)
|
|
|
608 --------------------------------------
|
|
|
609
|
|
|
610 Notable changes in bwa-short:
|
|
|
611
|
|
|
612 * Report multiple hits in the SAM format at a new tag XA encoded as:
|
|
|
613 (chr,pos,CIGAR,NM;)*. By default, if a paired or single-end read has
|
|
|
614 4 or fewer hits, they will all be reported; if a read in a anomalous
|
|
|
615 pair has 11 or fewer hits, all of them will be reported.
|
|
|
616
|
|
|
617 * Perform Smith-Waterman alignment also for anomalous read pairs when
|
|
|
618 both ends have quality higher than 17. This reduces false positives
|
|
|
619 for some SV discovery algorithms.
|
|
|
620
|
|
|
621 * Do not report "weird pairing" when the insert size distribution is
|
|
|
622 too fat or has a mean close to zero.
|
|
|
623
|
|
|
624 * If a read is bridging two adjacent chromsomes, flag it as unmapped.
|
|
|
625
|
|
|
626 * Fixed a small but long existing memory leak in paired-end mapping.
|
|
|
627
|
|
|
628 * Multiple bug fixes in SOLiD mapping: a) quality "-1" can be correctly
|
|
|
629 parsed by solid2fastq.pl; b) truncated quality string is resolved; c)
|
|
|
630 SOLiD read mapped to the reverse strand is complemented.
|
|
|
631
|
|
|
632 * Bwa now calculates skewness and kurtosis of the insert size
|
|
|
633 distribution.
|
|
|
634
|
|
|
635 * Deploy a Bayesian method to estimate the maximum distance for a read
|
|
|
636 pair considered to be paired properly. The method is proposed by
|
|
|
637 Gerton Lunter, but bwa only implements a simplified version.
|
|
|
638
|
|
|
639 * Export more functions for Java bindings, by Matt Hanna (See:
|
|
|
640 http://www.broadinstitute.org/gsa/wiki/index.php/Sting_BWA/C_bindings)
|
|
|
641
|
|
|
642 * Abstract bwa CIGAR for further extension, by Rodrigo Goya.
|
|
|
643
|
|
|
644 (0.5.6: 10 Feburary 2010, r1303)
|
|
|
645
|
|
|
646
|
|
|
647
|
|
|
648 Beta Release 0.5.5 (10 November, 2009)
|
|
|
649 --------------------------------------
|
|
|
650
|
|
|
651 This is a bug fix release:
|
|
|
652
|
|
|
653 * Fixed a serious bug/typo in aln which does not occur given short
|
|
|
654 reads, but will lead to segfault for >500bp reads. Of course, the aln
|
|
|
655 command is not recommended for reads longer than 200bp, but this is a
|
|
|
656 bug anyway.
|
|
|
657
|
|
|
658 * Fixed a minor bug/typo which leads to incorrect single-end mapping
|
|
|
659 quality when one end is moved to meet the mate-pair requirement.
|
|
|
660
|
|
|
661 * Fixed a bug in samse for mapping in the color space. This bug is
|
|
|
662 caused by quality filtration added since 0.5.1.
|
|
|
663
|
|
|
664 (0.5.5: 10 November 2009, r1273)
|
|
|
665
|
|
|
666
|
|
|
667
|
|
|
668 Beta Release 0.5.4 (9 October, 2009)
|
|
|
669 ------------------------------------
|
|
|
670
|
|
|
671 Since this version, the default seed length used in the "aln" command is
|
|
|
672 changed to 32.
|
|
|
673
|
|
|
674 Notable changes in bwa-short:
|
|
|
675
|
|
|
676 * Added a new tag "XC:i" which gives the length of clipped reads.
|
|
|
677
|
|
|
678 * In sampe, skip alignments in case of a bug in the Smith-Waterman
|
|
|
679 alignment module.
|
|
|
680
|
|
|
681 * In sampe, fixed a bug in pairing when the read sequence is identical
|
|
|
682 to its reverse complement.
|
|
|
683
|
|
|
684 * In sampe, optionally preload the entire FM-index into memory to
|
|
|
685 reduce disk operations.
|
|
|
686
|
|
|
687 Notable changes in dBWT-SW/BWA-SW:
|
|
|
688
|
|
|
689 * Changed name dBWT-SW to BWA-SW.
|
|
|
690
|
|
|
691 * Optionally use "hard clipping" in the SAM output.
|
|
|
692
|
|
|
693 (0.5.4: 9 October 2009, r1245)
|
|
|
694
|
|
|
695
|
|
|
696
|
|
|
697 Beta Release 0.5.3 (15 September, 2009)
|
|
|
698 ---------------------------------------
|
|
|
699
|
|
|
700 Fixed a critical bug in bwa-short: reads mapped to the reverse strand
|
|
|
701 are not complemented.
|
|
|
702
|
|
|
703 (0.5.3: 15 September 2009, r1225)
|
|
|
704
|
|
|
705
|
|
|
706
|
|
|
707 Beta Release 0.5.2 (13 September, 2009)
|
|
|
708 ---------------------------------------
|
|
|
709
|
|
|
710 Notable changes in bwa-short:
|
|
|
711
|
|
|
712 * Optionally trim reads before alignment. See the manual page on 'aln
|
|
|
713 -q' for detailed description.
|
|
|
714
|
|
|
715 * Fixed a bug in calculating the NM tag for a gapped alignment.
|
|
|
716
|
|
|
717 * Fixed a bug given a mixture of reads with some longer than the seed
|
|
|
718 length and some shorter.
|
|
|
719
|
|
|
720 * Print SAM header.
|
|
|
721
|
|
|
722 Notable changes in dBWT-SW:
|
|
|
723
|
|
|
724 * Changed the default value of -T to 30. As a result, the accuracy is a
|
|
|
725 little higher for short reads at the cost of speed.
|
|
|
726
|
|
|
727 (0.5.2: 13 September 2009, r1223)
|
|
|
728
|
|
|
729
|
|
|
730
|
|
|
731 Beta Release 0.5.1 (2 September, 2009)
|
|
|
732 --------------------------------------
|
|
|
733
|
|
|
734 Notable changes in the short read alignment component:
|
|
|
735
|
|
|
736 * Fixed a bug in samse: do not write mate coordinates.
|
|
|
737
|
|
|
738 Notable changes in dBWT-SW:
|
|
|
739
|
|
|
740 * Randomly choose one alignment if the read is a repetitive.
|
|
|
741
|
|
|
742 * Fixed a flaw when a read is mapped across two adjacent reference
|
|
|
743 sequences. However, wrong alignment reports may still occur rarely in
|
|
|
744 this case.
|
|
|
745
|
|
|
746 * Changed the default band width to 50. The speed is slower due to this
|
|
|
747 change.
|
|
|
748
|
|
|
749 * Improved the mapping quality a little given long query sequences.
|
|
|
750
|
|
|
751 (0.5.1: 2 September 2009, r1209)
|
|
|
752
|
|
|
753
|
|
|
754
|
|
|
755 Beta Release 0.5.0 (20 August, 2009)
|
|
|
756 ------------------------------------
|
|
|
757
|
|
|
758 This release implements a novel algorithm, dBWT-SW, specifically
|
|
|
759 designed for long reads. It is 10-50 times faster than SSAHA2, depending
|
|
|
760 on the characteristics of the input data, and achieves comparable
|
|
|
761 alignment accuracy while allowing chimera detection. In comparison to
|
|
|
762 BLAT, dBWT-SW is several times faster and much more accurate especially
|
|
|
763 when the error rate is high. Please read the manual page for more
|
|
|
764 information.
|
|
|
765
|
|
|
766 The dBWT-SW algorithm is kind of developed for future sequencing
|
|
|
767 technologies which produce much longer reads with a little higher error
|
|
|
768 rate. It is still at its early development stage. Some features are
|
|
|
769 missing and it may be buggy although I have evaluated on several
|
|
|
770 simulated and real data sets. But following the "release early"
|
|
|
771 paradigm, I would like the users to try it first.
|
|
|
772
|
|
|
773 Other notable changes in BWA are:
|
|
|
774
|
|
|
775 * Fixed a rare bug in the Smith-Waterman alignment module.
|
|
|
776
|
|
|
777 * Fixed a rare bug about the wrong alignment coordinate when a read is
|
|
|
778 poorly aligned.
|
|
|
779
|
|
|
780 * Fixed a bug in generating the "mate-unmap" SAM tag when both ends in
|
|
|
781 a pair are unmapped.
|
|
|
782
|
|
|
783 (0.5.0: 20 August 2009, r1200)
|
|
|
784
|
|
|
785
|
|
|
786
|
|
|
787 Beta Release 0.4.9 (19 May, 2009)
|
|
|
788 ---------------------------------
|
|
|
789
|
|
|
790 Interestingly, the integer overflow bug claimed to be fixed in 0.4.7 has
|
|
|
791 not in fact. Now I have fixed the bug. Sorry for this and thank Quan
|
|
|
792 Long for pointing out the bug (again).
|
|
|
793
|
|
|
794 (0.4.9: 19 May 2009, r1075)
|
|
|
795
|
|
|
796
|
|
|
797
|
|
|
798 Beta Release 0.4.8 (18 May, 2009)
|
|
|
799 ---------------------------------
|
|
|
800
|
|
|
801 One change to "aln -R". Now by default, if there are no more than '-R'
|
|
|
802 equally best hits, bwa will search for suboptimal hits. This change
|
|
|
803 affects the ability in finding SNPs in segmental duplications.
|
|
|
804
|
|
|
805 I have not tested this option thoroughly, but this simple change is less
|
|
|
806 likely to cause new bugs. Hope I am right.
|
|
|
807
|
|
|
808 (0.4.8: 18 May 2009, r1073)
|
|
|
809
|
|
|
810
|
|
|
811
|
|
|
812 Beta Release 0.4.7 (12 May, 2009)
|
|
|
813 ---------------------------------
|
|
|
814
|
|
|
815 Notable changes:
|
|
|
816
|
|
|
817 * Output SM (single-end mapping quality) and AM (smaller mapping
|
|
|
818 quality among the two ends) tag from sam output.
|
|
|
819
|
|
|
820 * Improved the functionality of stdsw.
|
|
|
821
|
|
|
822 * Made the XN tag more accurate.
|
|
|
823
|
|
|
824 * Fixed a very rare segfault caused by integer overflow.
|
|
|
825
|
|
|
826 * Improve the insert size estimation.
|
|
|
827
|
|
|
828 * Fixed compiling errors for some Linux systems.
|
|
|
829
|
|
|
830 (0.4.7: 12 May 2009, r1066)
|
|
|
831
|
|
|
832
|
|
|
833
|
|
|
834 Beta Release 0.4.6 (9 March, 2009)
|
|
|
835 ----------------------------------
|
|
|
836
|
|
|
837 This release improves the SOLiD support. First, a script for converting
|
|
|
838 SOLiD raw data is provided. This script is adapted from solid2fastq.pl
|
|
|
839 in the MAQ package. Second, a nucleotide reference file can be directly
|
|
|
840 used with 'bwa index'. Third, SOLiD paired-end support is
|
|
|
841 completed. Fourth, color-space reads will be converted to nucleotides
|
|
|
842 when SAM output is generated. Color errors are corrected in this
|
|
|
843 process. Please note that like MAQ, BWA cannot make use of the primer
|
|
|
844 base and the first color.
|
|
|
845
|
|
|
846 In addition, the calculation of mapping quality is also improved a
|
|
|
847 little bit, although end-users may barely observe the difference.
|
|
|
848
|
|
|
849 (0.4.6: 9 March 2009, r915)
|
|
|
850
|
|
|
851
|
|
|
852
|
|
|
853 Beta Release 0.4.5 (18 Feburary, 2009)
|
|
|
854 --------------------------------------
|
|
|
855
|
|
|
856 Not much happened, but I think it would be good to let the users use the
|
|
|
857 latest version.
|
|
|
858
|
|
|
859 Notable changes (Thank Bob Handsaker for catching the two bugs):
|
|
|
860
|
|
|
861 * Improved bounary check. Previous version may still give incorrect
|
|
|
862 alignment coordinates in rare cases.
|
|
|
863
|
|
|
864 * Fixed a bug in SW alignment when no residue matches. This only
|
|
|
865 affects the 'sampe' command.
|
|
|
866
|
|
|
867 * Robustly estimate insert size without setting the maximum on the
|
|
|
868 command line. Since this release 'sampe -a' only has an effect if
|
|
|
869 there are not enough good pairs to infer the insert size
|
|
|
870 distribution.
|
|
|
871
|
|
|
872 * Reduced false PE alignments a little bit by using the inferred insert
|
|
|
873 size distribution. This fix may be more important for long insert
|
|
|
874 size libraries.
|
|
|
875
|
|
|
876 (0.4.5: 18 Feburary 2009, r829)
|
|
|
877
|
|
|
878
|
|
|
879
|
|
|
880 Beta Release 0.4.4 (15 Feburary, 2009)
|
|
|
881 --------------------------------------
|
|
|
882
|
|
|
883 This is mainly a bug fix release. Notable changes are:
|
|
|
884
|
|
|
885 * Imposed boundary check for extracting subsequence from the
|
|
|
886 genome. Previously this causes memory problem in rare cases.
|
|
|
887
|
|
|
888 * Fixed a bug in failing to find whether an alignment overlapping with
|
|
|
889 N on the genome.
|
|
|
890
|
|
|
891 * Changed MD tag to meet the latest SAM specification.
|
|
|
892
|
|
|
893 (0.4.4: 15 Feburary 2009, r815)
|
|
|
894
|
|
|
895
|
|
|
896
|
|
|
897 Beta Release 0.4.3 (22 January, 2009)
|
|
|
898 ------------------------------------
|
|
|
899
|
|
|
900 Notable changes:
|
|
|
901
|
|
|
902 * Treat an ambiguous base N as a mismatch. Previous versions will not
|
|
|
903 map reads containing any N.
|
|
|
904
|
|
|
905 * Automatically choose the maximum allowed number of differences. This
|
|
|
906 is important when reads of different lengths are mixed together.
|
|
|
907
|
|
|
908 * Print mate coordinate if only one end is unmapped.
|
|
|
909
|
|
|
910 * Generate MD tag. This tag encodes the mismatching positions and the
|
|
|
911 reference bases at these positions. Deletions from the reference will
|
|
|
912 also be printed.
|
|
|
913
|
|
|
914 * Optionally dump multiple hits from samse, in another concise format
|
|
|
915 rather than SAM.
|
|
|
916
|
|
|
917 * Optionally disable iterative search. This is VERY SLOOOOW, though.
|
|
|
918
|
|
|
919 * Fixed a bug in generate SAM.
|
|
|
920
|
|
|
921 (0.4.3: 22 January 2009, r787)
|
|
|
922
|
|
|
923
|
|
|
924
|
|
|
925 Beta Release 0.4.2 (9 January, 2009)
|
|
|
926 ------------------------------------
|
|
|
927
|
|
|
928 Aaron Quinlan found a bug in the indexer: the bwa indexer segfaults if
|
|
|
929 there are no comment texts in the FASTA header. This is a critical
|
|
|
930 bug. Nothing else was changed.
|
|
|
931
|
|
|
932 (0.4.2: 9 January 2009, r769)
|
|
|
933
|
|
|
934
|
|
|
935
|
|
|
936 Beta Release 0.4.1 (7 January, 2009)
|
|
|
937 ------------------------------------
|
|
|
938
|
|
|
939 I am sorry for the quick updates these days. I like to set a milestone
|
|
|
940 for BWA and this release seems to be. For paired end reads, BWA also
|
|
|
941 does Smith-Waterman alignment for an unmapped read whose mate can be
|
|
|
942 mapped confidently. With this strategy BWA achieves similar accuracy to
|
|
|
943 maq. Benchmark is also updated accordingly.
|
|
|
944
|
|
|
945 (0.4.1: 7 January 2009, r760)
|
|
|
946
|
|
|
947
|
|
|
948
|
|
|
949 Beta Release 0.4.0 (6 January, 2009)
|
|
|
950 ------------------------------------
|
|
|
951
|
|
|
952 In comparison to the release two days ago, this release is mainly tuned
|
|
|
953 for performance with some tricks I learnt from Bowtie. However, as the
|
|
|
954 indexing format has also been changed, I have to increase the version
|
|
|
955 number to 0.4.0 to emphasize that *DATABASE MUST BE RE-INDEXED* with
|
|
|
956 'bwa index'.
|
|
|
957
|
|
|
958 * Improved the speed by about 20%.
|
|
|
959
|
|
|
960 * Added multi-threading to 'bwa aln'.
|
|
|
961
|
|
|
962 (0.4.0: 6 January 2009, r756)
|
|
|
963
|
|
|
964
|
|
|
965
|
|
|
966 Beta Release 0.3.0 (4 January, 2009)
|
|
|
967 ------------------------------------
|
|
|
968
|
|
|
969 * Added paired-end support by separating SA calculation and alignment
|
|
|
970 output.
|
|
|
971
|
|
|
972 * Added SAM output.
|
|
|
973
|
|
|
974 * Added evaluation to the documentation.
|
|
|
975
|
|
|
976 (0.3.0: 4 January 2009, r741)
|
|
|
977
|
|
|
978
|
|
|
979
|
|
|
980 Beta Release 0.2.0 (15 Augusst, 2008)
|
|
|
981 -------------------------------------
|
|
|
982
|
|
|
983 * Take the subsequence at the 5'-end as seed. Seeding strategy greatly
|
|
|
984 improves the speed for long reads, at the cost of missing a few true
|
|
|
985 hits that contain many differences in the seed. Seeding also increase
|
|
|
986 the memory by 800MB.
|
|
|
987
|
|
|
988 * Fixed a bug which may miss some gapped alignments. Fixing the bug
|
|
|
989 also slows the speed a little.
|
|
|
990
|
|
|
991 (0.2.0: 15 August 2008, r428)
|
|
|
992
|
|
|
993
|
|
|
994
|
|
|
995 Beta Release 0.1.6 (08 Augusst, 2008)
|
|
|
996 -------------------------------------
|
|
|
997
|
|
|
998 * Give accurate CIGAR string.
|
|
|
999
|
|
|
1000 * Add a simple interface to SW/NW alignment
|
|
|
1001
|
|
|
1002 (0.1.6: 08 August 2008, r414)
|
|
|
1003
|
|
|
1004
|
|
|
1005
|
|
|
1006 Beta Release 0.1.5 (27 July, 2008)
|
|
|
1007 ----------------------------------
|
|
|
1008
|
|
|
1009 * Improve the speed. This version is expected to give the same results.
|
|
|
1010
|
|
|
1011 (0.1.5: 27 July 2008, r400)
|
|
|
1012
|
|
|
1013
|
|
|
1014
|
|
|
1015 Beta Release 0.1.4 (22 July, 2008)
|
|
|
1016 ----------------------------------
|
|
|
1017
|
|
|
1018 * Fixed a bug which may cause missing gapped alignments.
|
|
|
1019
|
|
|
1020 * More clearly define what alignments can be found by BWA (See
|
|
|
1021 manual). Now BWA runs a little slower because it will visit more
|
|
|
1022 potential gapped alignments.
|
|
|
1023
|
|
|
1024 * A bit code clean up.
|
|
|
1025
|
|
|
1026 (0.1.4: 22 July 2008, r387)
|
|
|
1027
|
|
|
1028
|
|
|
1029
|
|
|
1030 Beta Release 0.1.3 (21 July, 2008)
|
|
|
1031 ----------------------------------
|
|
|
1032
|
|
|
1033 Improve the speed with some tricks on retrieving occurences. The results
|
|
|
1034 should be exactly the same as that of 0.1.2.
|
|
|
1035
|
|
|
1036 (0.1.3: 21 July 2008, r382)
|
|
|
1037
|
|
|
1038
|
|
|
1039
|
|
|
1040 Beta Release 0.1.2 (17 July, 2008)
|
|
|
1041 ----------------------------------
|
|
|
1042
|
|
|
1043 Support gapped alignment. Codes for ungapped alignment has been removed.
|
|
|
1044
|
|
|
1045 (0.1.2: 17 July 2008, r371)
|
|
|
1046
|
|
|
1047
|
|
|
1048
|
|
|
1049 Beta Release 0.1.1 (03 June, 2008)
|
|
|
1050 -----------------------------------
|
|
|
1051
|
|
|
1052 This is the first release of BWA, Burrows-Wheeler Alignment tool. Please
|
|
|
1053 read man page for more information about this software.
|
|
|
1054
|
|
|
1055 (0.1.1: 03 June 2008, r349)
|
