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comparison exomedepth.xml @ 8:5d60331757d3 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
author iuc
date Wed, 25 Nov 2020 18:37:13 +0000
parents 45af4a9748cf
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7:45af4a9748cf 8:5d60331757d3
101 101
102 **What ExomeDepth does and does not do** 102 **What ExomeDepth does and does not do**
103 103
104 ExomeDepth uses read depth data to call CNVs from exome sequencing experiments. A key idea is that the test 104 ExomeDepth uses read depth data to call CNVs from exome sequencing experiments. A key idea is that the test
105 exome should be compared to a matched aggregate reference set. This aggregate reference set should combine 105 exome should be compared to a matched aggregate reference set. This aggregate reference set should combine
106 exomes from the same batch and it should also be optimized for each exome. It will certainly differ from one exome 106 exomes from the same batch and it should also be optimized for each exome. It will certainly differ from one exome
107 to the next. 107 to the next.
108 108
109 Importantly, ExomeDepth assumes that the CNV of interest is absent from the aggregate reference set. Hence 109 Importantly, ExomeDepth assumes that the CNV of interest is absent from the aggregate reference set. Hence
110 related individuals should be excluded from the aggregate reference. It also means that ExomeDepth can miss 110 related individuals should be excluded from the aggregate reference. It also means that ExomeDepth can miss
111 common CNVs, if the call is also present in the aggregate reference. ExomeDepth is really suited to detect rare 111 common CNVs, if the call is also present in the aggregate reference. ExomeDepth is really suited to detect rare
112 CNV calls (typically for rare Mendelian disorder analysis). 112 CNV calls (typically for rare Mendelian disorder analysis).
113 113
114 The ideas used in this package are of course not specific to exome sequencing and could be applied to other 114 The ideas used in this package are of course not specific to exome sequencing and could be applied to other
115 targeted sequencing datasets, as long as they contain a sufficiently large number of exons to estimate the parameters 115 targeted sequencing datasets, as long as they contain a sufficiently large number of exons to estimate the parameters
116 (at least 20 genes, say, but probably more would be useful). Also note that PCR based enrichment studies are often 116 (at least 20 genes, say, but probably more would be useful). Also note that PCR based enrichment studies are often
117 not well suited for this type of read depth analysis. The reason is that as the number of cycles is often set to a high 117 not well suited for this type of read depth analysis. The reason is that as the number of cycles is often set to a high
118 number in order to equalize the representation of each amplicon, which can discard the CNV information. 118 number in order to equalize the representation of each amplicon, which can discard the CNV information.
119 ]]></help> 119 ]]></help>
120 <citations> 120 <citations>