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comparison tools/naive_variant_detector.xml @ 21:69d5400f3186 default tip

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update readme
author Daniel Blankenberg <dan@bx.psu.edu>
date Tue, 27 Aug 2013 14:54:49 -0400
parents 7f654ba273cb
children
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20:66a4325d9394 21:69d5400f3186
124 **Outputs** 124 **Outputs**
125 125
126 The output is in VCF format. 126 The output is in VCF format.
127 127
128 Example VCF output line, without reporting by strand: 128 Example VCF output line, without reporting by strand:
129 ``chrM 16029 . T G,A,C . . AC=15,9,5;AF=0.00155311658729,0.000931869952371,0.000517705529095 GT:AC:AF:NC 0/0:15,9,5:0.00155311658729,0.000931869952371,0.000517705529095:A=9,C=5,T=9629,G=15,`` 129 ``chrM 16029 . T G,A,C . . AC=15,9,5;AF=0.00155311658729,0.000931869952371,0.000517705529095 GT:AC:AF:NC 0/0:15,9,5:0.00155311658729,0.000931869952371,0.000517705529095:A=9,C=5,T=9629,G=15,``
130 130
131 Example VCF output line, when reporting by strand: 131 Example VCF output line, when reporting by strand:
132 ``chrM 16029 . T G,A,C . . AC=15,9,5;AF=0.00155311658729,0.000931869952371,0.000517705529095 GT:AC:AF:NC 0/0:15,9,5:0.00155311658729,0.000931869952371,0.000517705529095:+T=3972,-A=9,-C=5,-T=5657,-G=15,`` 132 ``chrM 16029 . T G,A,C . . AC=15,9,5;AF=0.00155311658729,0.000931869952371,0.000517705529095 GT:AC:AF:NC 0/0:15,9,5:0.00155311658729,0.000931869952371,0.000517705529095:+T=3972,-A=9,-C=5,-T=5657,-G=15,``
133 133
134 **Options** 134 **Options**
135 135
136 Reference Genome: 136 Reference Genome:
137 137
138 Ensure that you have selected the correct reference genome, either from the list of built-in genomes or by selecting the corresponding FASTA file from your history. 138 Ensure that you have selected the correct reference genome, either from the list of built-in genomes or by selecting the corresponding FASTA file from your history.
139 139
140 Restrict to regions: 140 Restrict to regions:
141 141
142 You can specify any number of regions on which you would like to receive results. You can specify just a chromosome name, or a chromosome name and start postion, or a chromosome name and start and end position for the set of desired regions. 142 You can specify any number of regions on which you would like to receive results. You can specify just a chromosome name, or a chromosome name and start postion, or a chromosome name and start and end position for the set of desired regions.
143 143
144 Minimum number of reads needed to consider a REF/ALT: 144 Minimum number of reads needed to consider a REF/ALT:
145 145
146 This value declares the minimum number of reads containing a particular base at each position in order to list and use said allele in genotyping calls. Default is 0. 146 This value declares the minimum number of reads containing a particular base at each position in order to list and use said allele in genotyping calls. Default is 0.
147 147
148 Minimum base quality: 148 Minimum base quality:
149 149
150 The minimum base quality score needed for the position in a read to be used for nucleotide counts and genotyping. Default is no filter. 150 The minimum base quality score needed for the position in a read to be used for nucleotide counts and genotyping. Default is no filter.
151 151
152 Minimum mapping quality: 152 Minimum mapping quality:
153 153
154 The minimum mapping quality score needed to consider a read for nucleotide counts and genotyping. Default is no filter. 154 The minimum mapping quality score needed to consider a read for nucleotide counts and genotyping. Default is no filter.
155 155
156 Ploidy: 156 Ploidy:
157 157
158 The number of genotype calls to make at each reported position. 158 The number of genotype calls to make at each reported position.
159 159
160 Only write out positions with with possible alternate alleles: 160 Only write out positions with with possible alternate alleles:
161 161
162 When set, only positions which have at least one non-reference nucleotide which passes declare filters will be present in the output. 162 When set, only positions which have at least one non-reference nucleotide which passes declare filters will be present in the output.
163 163
164 Report counts by strand: 164 Report counts by strand:
165 165
166 When set, nucleotide counts (NC) will be reported in reference to the aligned read's source strand. Reported as: &lt;strand&gt;&lt;BASE&gt;=&lt;COUNT&gt;. 166 When set, nucleotide counts (NC) will be reported in reference to the aligned read's source strand. Reported as: &lt;strand&gt;&lt;BASE&gt;=&lt;COUNT&gt;.
167 167
168 Choose the dtype to use for storing coverage information: 168 Choose the dtype to use for storing coverage information:
169 169
170 This controls the maximum depth value for each nucleotide/position/strand (when specified). Smaller values require the least amount of memory, but have smaller maximal limits. 170 This controls the maximum depth value for each nucleotide/position/strand (when specified). Smaller values require the least amount of memory, but have smaller maximal limits.
171 171
172 +--------+----------------------------+ 172 +--------+----------------------------+
173 | name | maximum coverage value | 173 | name | maximum coverage value |
174 +========+============================+ 174 +========+============================+
175 | uint8 | 255 | 175 | uint8 | 255 |
176 +--------+----------------------------+ 176 +--------+----------------------------+
177 | uint16 | 65,535 | 177 | uint16 | 65,535 |
178 +--------+----------------------------+ 178 +--------+----------------------------+
179 | uint32 | 4,294,967,295 | 179 | uint32 | 4,294,967,295 |
180 +--------+----------------------------+ 180 +--------+----------------------------+
181 | uint64 | 18,446,744,073,709,551,615 | 181 | uint64 | 18,446,744,073,709,551,615 |
182 +--------+----------------------------+ 182 +--------+----------------------------+
183 183
184 ------ 184 ------
185 185
186 **Citation** 186 **Citation**
187 187