annotate bamCompare.xml @ 5:c54d31467be4 draft

Uploaded
author bgruening
date Fri, 29 Nov 2013 08:59:04 -0500
parents d957e25e18a3
children c53a73b8eef9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
1 <tool id="deeptools_bamCompare" name="bamCompare" version="1.0">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
2 <description>normalizes and compares two BAM files to obtain the ratio, log2ratio or difference. (bam2bigwig)</description>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
3 <expand macro="requirements" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
4 <macros>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
5 <import>deepTools_macros.xml</import>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
6 </macros>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
7 <command>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
8 bamCompare
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
9
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
10 @THREADS@
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
11
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
12 --bamfile1 '$bamFile1'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
13 -bai1 '${bamFile1.metadata.bam_index}'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
14 --bamfile2 '$bamFile2'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
15 -bai2 '${bamFile2.metadata.bam_index}'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
16
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
17 --outFileName '$outFileName'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
18 --outFileFormat '$outFileFormat'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
19
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
20 --fragmentLength $fragmentLength
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
21 --binSize $binSize
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
22
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
23 #if $scaling.method == 'SES':
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
24 --scaleFactorsMethod SES
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
25 --sampleLength $scaling.sampleLength
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
26 #elif $scaling.method == 'readCount':
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
27 --scaleFactorsMethod readCount
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
28 #elif $scaling.method == 'own':
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
29 --scaleFactors '$scaling.scaleFactor1:$scaling.scaleFactor2'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
30 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
31
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
32 --ratio $comparison.type
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
33
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
34 #if $comparison.type=='subtract':
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
35 #if $comparison.normalization.type=='rpkm':
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
36 --normalizeUsingRPKM
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
37 #elif $comparison.normalization.type=='1x':
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
38 --normalizeTo1x $comparison.normalization.normalizeTo1x
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
39 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
40
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
41 #if str($comparison.ignoreForNormalization).strip() != '':
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
42 --ignoreForNormalization $comparison.ignoreForNormalization
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
43 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
44
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
45 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
46
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
47 #if $advancedOpt.showAdvancedOpt == "yes":
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
48 #if $advancedOpt.smoothLength:
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
49 --smoothLength '$advancedOpt.smoothLength'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
50 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
51
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
52 #if str($advancedOpt.region.value) != '':
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
53 --region '$advancedOpt.region'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
54 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
55
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
56 $advancedOpt.doNotExtendPairedEnds
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
57 $advancedOpt.ignoreDuplicates
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
58
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
59 #if $advancedOpt.minMappingQuality:
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
60 --minMappingQuality '$advancedOpt.minMappingQuality'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
61 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
62
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
63 --missingDataAsZero $advancedOpt.missingDataAsZero
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
64
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
65 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
66
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
67 </command>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
68
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
69 <inputs>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
70 <param name="bamFile1" format="bam" type="data" label="Treatment BAM file"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
71 help="The BAM file must be sorted."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
72
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
73 <param name="bamFile2" format="bam" type="data" label="Input BAM file"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
74 help="The BAM file must be sorted."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
75
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
76 <param name="fragmentLength" type="integer" value="300" min="1"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
77 label="Length of the average fragment size"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
78 help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see &quot;normalize coverage to 1x&quot;). The formula to normalize using the sequencing depth is genomeSize/(number of mapped reads * fragment length). *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
79
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
80 <param name="binSize" type="integer" value="50" min="1"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
81 label="Bin size in bp"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
82 help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads) will be reported. If only half a fragment overlaps, this fraction will be reported. "/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
83
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
84 <conditional name="scaling">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
85 <param name="method" type="select"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
86 label="Method to use for scaling the largest sample to the smallest">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
87 <option value="readCount" selected="true">read count</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
88 <option value="SES">signal extraction scaling (SES)</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
89 <option value="own">enter own scaling factors</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
90 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
91 <when value="SES">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
92 <param name="sampleLength" type="integer" value="1000" min="10"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
93 label="Length in base pairs used to sample the genome and compute the size or scaling factors to compare the two BAM files "
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
94 help="The default is fine. Only change it if you know what you are doing" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
95 </when>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
96 <when value="readCount" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
97 <when value="own">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
98 <param name="scaleFactor1" type="float" value="1"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
99 label="Scale factor for treatment"/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
100
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
101 <param name="scaleFactor2" type="float" value="1"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
102 label="Scale factor for input"/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
103 </when>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
104 </conditional>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
105
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
106 <conditional name="comparison">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
107 <param name="type" type="select"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
108 label="How to compare the two files">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
109 <option value="log2" selected="true">compute log2 of the number of reads ratio</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
110 <option value="ratio">compute the ratio of the number of reads</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
111 <option value="subtract">compute difference (subtract input from treatment) of the number of reads</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
112 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
113 <when value="log2" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
114 <when value="ratio" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
115 <when value="subtract">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
116 <conditional name="normalization">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
117 <param name="type" type="select" label="Normalization method" >
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
118 <option value="1x">Normalize coverage to 1x</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
119 <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
120 <option value="no">Do not normalize or scale</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
121 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
122 <when value="rpkm" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
123 <when value="no" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
124 <when value="1x">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
125 <param name="normalizeTo1x" type="integer" value="2150570000"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
126 label="Report normalized coverage to 1x sequenceing depth"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
127 help ="Sequencing depth is defined as the total number of mapped reads * fragment length / effective genome size. To use this option, the effective genome size has to be given. Common values are: mm9: 2150570000, hg19:2451960000, dm3:121400000 and ce10:93260000."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
128 </when>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
129 </conditional>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
130 <param name="ignoreForNormalization" type="text" value="" size="50"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
131 label="regions that should be excluded for calculating the scaling factor"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
132 help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor. For example, if you know some regions that you suspect to be present more often in your sample's genome than in the reference genome that will therefore accumulate reads (CNV). Another typical example is the single X chromosome in male samples that should be scaled separately from the diploid autosomes. For example chrX,chrY,chr3. or chr10:12220-128932" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
133 </when>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
134 </conditional>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
135
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
136 <param name="outFileFormat" type="select" label="Coverage file format">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
137 <option value="bigwig" selected="true">bigwig</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
138 <option value="bedgraph">bedgraph</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
139 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
140
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
141 <conditional name="advancedOpt">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
142 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
143 <option value="no" selected="true">no</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
144 <option value="yes">yes</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
145 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
146 <when value="no" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
147 <when value="yes">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
148
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
149 <param name="smoothLength" type="integer" value="1" optional="true" min="1"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
150 label="Smooth values using the following length (in bp)"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
151 help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
152
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
153 <param name="region" type="text" value=""
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
154 label="Region of the genome to limit the operation to"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
155 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
156
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
157 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
158 label="Do not extend paired ends"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
159 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
160
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
161 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
162 label="Ignore duplicates"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
163 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
164
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
165 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
166 label="Minimum mapping quality (e.g. BOWTIE2 measures)"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
167 help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
168
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
169 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
170 label ="Treat missing data as zero"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
171 help ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
172 </when>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
173 </conditional>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
174
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
175 </inputs>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
176 <outputs>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
177 <data format="bigwig" name="outFileName">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
178 <change_format>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
179 <when input="outFileFormat" value="bigwig" format="bigwig" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
180 <when input="outFileFormat" value="bedgraph" format="bedgraph" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
181 </change_format>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
182 </data>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
183 </outputs>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
184 <help>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
185
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
186 **What it does**
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
187
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
188 This tool compares two BAM files based on the number of mapped reads. To
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
189 compare the BAM files, the genome is partitioned into bins of equal size,
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
190 the reads are counted for each bin and each BAM file and finally, a summarizing value is reported.
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
191 This value can be the ratio of the number of reads per bin, the log2 of the ratio or the difference.
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
192 This tool can normalize the number of reads on each BAM file using the SES method
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
193 proposed by Diaz et al. (2012). Stat Appl Genet Mol Biol 11(3). Normalization based on read counts is also available. The
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
194 output is either a bedGraph or a bigWig file containing the bin location and
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
195 the resulting comparison values.
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
196 If paired-end reads are present, the fragment
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
197 length reported in the BAM file is used by default.
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
198
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
199
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
200 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
201
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
202
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
203 **Output files**:
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
204
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
205 - same as for bamCoverage, except that you now obtain 1 coverage file that is based on 2 BAM files.
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
206
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
207 -----
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
208
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
209 .. class:: infomark
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
210
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
211 </help>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
212 </tool>