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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/snpeff">Debian Med / snpeff</a>
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Commits:
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<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/0b6a8a8782a44c45d3f70339102b2e67130ef3e4">0b6a8a87</a></strong>
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<span>by Steffen Möller</span>
<i>at 2021-03-30T16:01:25+00:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update control - extended description</pre>
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<h4>1 changed file:</h4>
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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/snpeff/-/commit/0b6a8a8782a44c45d3f70339102b2e67130ef3e4#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -66,11 +66,29 @@ Architecture: all</td>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext">Depends: ${java:Depends},</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"> libsnpeff-java (= ${binary:Version})</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">Suggests: vcfanno</span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext">Description: genetic variant annotation and effect prediction toolbox - tool</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> "We are all different!" Geneticists agree to this old Monty Python joke.</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> Even twins, who are said to be identical are on a molecular</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> level only "mostly" identical. And even within the exact same individual,</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> healthy cells acquire mutations such that we are all genetic mosaics.</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> This happens upon environmental factors, e.g. like UV light, but also</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> as random mishaps during cellular divisions.</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> Because there are so many genetic differences, and most have just no</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> particular meaning for the development of a phenotype, i.e. most have no</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> effect, it would be nice to have heuristics implemented that direct the</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> researcher towards single-nucleotide polymorphisms (SNPs) that are most</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> likely to be relevant. This identifies the gene that causes or contributes</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> to, e.g, an illness, and possibly also genes that are affected by that</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> change. Such mechanistic understanding of a disease, particularly when</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> multiple genes and multiple genetic variants are contributing to the</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> then "polgygenic" phenotype, is at the onset of drug development and</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> increasingly also for selecting individualize therapies in the clinic.</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext"> SnpEff is a variant annotation and effect prediction tool. It annotates</span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext"> and predicts the effects of variants on genes (such as amino acid</span>
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext"> changes).</span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext"> The inputs are predicted variants (SNPs, insertions, deletions and</span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext"> MNPs). The input file is usually obtained as a result of a sequencing</span>
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76
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext"> experiment, and it is usually in variant call format (VCF).</span>
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