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