Search Results for "snpeff"

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.

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): CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, SAMPLE_ID, ... ...

...These complex mutations consist of two or more consecutive nucleotide substitutions, but can only be detected in the format of several single nucleotide variations (SNV) by most variant callers and annotated separately, which likely leads to incorrect amino acid prediction when more than one mutated bases occur within the same protein codon. MAC screens through a list 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.