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Showing 3 open source projects for "snpeff"
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snpEff is a fast variant effect predictor (SNP, MNP and InDels) for genomic data. It is integrated with Galaxy so it can be used either as a command line or as a web application.
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denovo_hit
Outputs potential denovo variants from VCF given pedigree information.
Program takes variants calls and determines if the call is novel for a child compared to parents. Program can handle both annotated and unannotated VCF files, however output file is not compatible with GATK's snpEff, so you should annotate prior to using denovo_hit. Usage: ./denovo_hit <VCF file> <PED file> Output: ./potential_denovo.txt To compile: g++ -std=c++11 denovo_hit.cpp -o denovo_hit Please see files for example VCF file, and pedigree file. Format VCF file (tab delimited... -
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MNV Annotation Corrector
Multi-nucleotide Variation Annotation Corrector for NGS SNV callers
... of user-provided SNVs and the matching BAM file to accurately identify MNV, and use existing annotators (currently supports ANNOVAR/SnpEff/VEP) to provide corrected amino acid prediction.
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