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comparison snpEff.xml @ 12:5a29ab10dba6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71
author iuc
date Thu, 29 Mar 2018 20:39:49 -0400
parents 5b4ac70948d2
children 85ca751407c3
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11:bfa6c1b8a03c 12:5a29ab10dba6
1 <tool id="snpEff" name="SnpEff eff:" version="@wrapper_version@.1"> 1 <tool id="snpEff" name="SnpEff eff:" version="@wrapper_version@.galaxy1">
2 <description> annotate variants</description> 2 <description> annotate variants</description>
3 <macros> 3 <macros>
4 <import>snpEff_macros.xml</import> 4 <import>snpEff_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
384 - **Input**: The inputs are predicted variants (SNPs, insertions, deletions and MNPs). The input file is usually obtained as a result of a sequencing experiment, and it is usually in variant call format (VCF). 384 - **Input**: The inputs are predicted variants (SNPs, insertions, deletions and MNPs). The input file is usually obtained as a result of a sequencing experiment, and it is usually in variant call format (VCF).
385 - **Output**: SnpEff analyzes the input variants. It annotates the variants and calculates the effects they produce on known genes (e.g. amino acid changes). A list of effects and annotations that SnpEff can calculate can be found here. 385 - **Output**: SnpEff analyzes the input variants. It annotates the variants and calculates the effects they produce on known genes (e.g. amino acid changes). A list of effects and annotations that SnpEff can calculate can be found here.
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387 By genetic variant we mean difference between a genome and a "reference" genome. As an example, imagine we are sequencing a "sample". Here "sample" can mean anything that you are interested in studying, from a cell culture, to a mouse or a cancer patient. It is a standard procedure to compare your sample sequences against the corresponding "reference genome". For instance you may compare the cancer patient genome against the "reference genome". 387 By genetic variant we mean difference between a genome and a "reference" genome. As an example, imagine we are sequencing a "sample". Here "sample" can mean anything that you are interested in studying, from a cell culture, to a mouse or a cancer patient. It is a standard procedure to compare your sample sequences against the corresponding "reference genome". For instance you may compare the cancer patient genome against the "reference genome".
388 388
389 In a typical sequencing experiment, you will find many places in the genome where your sample differs from the reference genome. These are called "genomic variants" or just "variants". 389 In a typical sequencing experiment, you will find many places in the genome where your sample differs from the reference genome. These are called "genomic variants" or just "variants".
390 Typically, variants are categorized as follows: 390 Typically, variants are categorized as follows:
391 391
392 - SNP (Single-Nucleotide Polymorphism) Reference = 'A', Sample = 'C' 392 - SNP (Single-Nucleotide Polymorphism) Reference = 'A', Sample = 'C'
393 - Ins (Insertion) Reference = 'A', Sample = 'AGT' 393 - Ins (Insertion) Reference = 'A', Sample = 'AGT'
394 - Del (Deletion) Reference = 'AC', Sample = 'C' 394 - Del (Deletion) Reference = 'AC', Sample = 'C'
395 - MNP (Multiple-nucleotide polymorphism) Reference = 'ATA', Sample = 'GTC' 395 - MNP (Multiple-nucleotide polymorphism) Reference = 'ATA', Sample = 'GTC'
396 - MIXED (Multiple-nucleotide and an InDel) Reference = 'ATA', Sample = 'GTCAGT' 396 - MIXED (Multiple-nucleotide and an InDel) Reference = 'ATA', Sample = 'GTCAGT'
397 397
398 This is not a comprehensive list, it is just to give you an idea. 398 This is not a comprehensive list, it is just to give you an idea.
399 399
400 Suppose you have a huge file describing all the differences between your sample and the reference genome. But you want to know more about these variants than just their genetic coordinates. E.g.: Are they in a gene? In an exon? Do they change protein coding? Do they cause premature stop codons? SnpEff can help you answer all these questions. The process of adding this information about the variants is called "Annotation". 400 Suppose you have a huge file describing all the differences between your sample and the reference genome. But you want to know more about these variants than just their genetic coordinates. E.g.: Are they in a gene? In an exon? Do they change protein coding? Do they cause premature stop codons? SnpEff can help you answer all these questions. The process of adding this information about the variants is called "Annotation".
401 SnpEff provides several degrees of annotations, from simple (e.g. which gene is each variant affecting) to extremely complex annotations (e.g. will this non-coding variant affect the expression of a gene?). It should be noted that the more complex the annotations, the more it relies in computational predictions. Such computational predictions can be incorrect, so results from SnpEff (or any prediction algorithm) cannot be trusted blindly, they must be analyzed and independently validated by corresponding wet-lab experiments. 401 SnpEff provides several degrees of annotations, from simple (e.g. which gene is each variant affecting) to extremely complex annotations (e.g. will this non-coding variant affect the expression of a gene?). It should be noted that the more complex the annotations, the more it relies in computational predictions. Such computational predictions can be incorrect, so results from SnpEff (or any prediction algorithm) cannot be trusted blindly, they must be analyzed and independently validated by corresponding wet-lab experiments.
402 402
403 @snpeff_in_galaxy_info@ 403 @snpeff_in_galaxy_info@
404 @external_documentation@ 404 @external_documentation@
405 ]]> 405 ]]>