VIP - Variant Identification Pipeline | Tool name | VIP - Variant Identification Pipeline |
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| URL | http://athos.ugent.be/VIP_pipeline |
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| Important features | 1. Used for mapping, SNP calling, coverage analysis and SNP annotation.
2. Used for analysis of 454/Roche GS-FLX amplicon re-sequencing experiments that enables variation detection, variation detection validation, PCR efficiency optimization and allows optimization of the multiplex PCR, used to amplify the amplicons. |
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| Citations | De Schrijver JM, De Leeneer K, Lefever S, Sabbe N, Pattyn F, Van Nieuwerburgh F, Coucke P, Deforce D, Vandesompele J, Bekaert S, Hellemans J, Van Criekinge W. Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline. BMC Bioinformatics. 2010 May 20;11:269. PubMed PMID: 20487544; PubMed Central PMCID: PMC2880033. |
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| Year of publication | 2010 |
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| Rank by usage frequency | 100 |
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| Comments | |
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| Function | SNP discovery, Structural variant discovery, Software package |
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| Category | Free, Downloadable |
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| License | GNU GPL V3 |
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| Status | |
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| Input file format | FASTA and Qual sequence files |
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| Output file format | Output to local
database |
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| Operating system | Linux 64bit |
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| Operating language |
Perl, BLAT and a MySQL5 |
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| Platform | 454/Roche GS-FLX |
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| Maintained by | |
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| Downloadable file format | |
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| Submission file format | |
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