snpEff 2.0.4 RC 1

What is snpEff?<br />It's a variant effect predictor tool, it predicts the effect of genetic variations (SNPs, insertions, deletions and MNPs).<br /> Release Candidate 1<br />Take a look at all the new features added<br /><br /> Database download command, e.g. "java -jar snpEff.jar download GRCH37.64"<br /> RefSeq annotations support added.<br /> Rogue transcript filter: By default SnpEff filters out some suspicious transcripts from annotations databases. This should improve false positive rates.<br /> Amino acid changes in HGVS style (VCF output)<br /> SnpSift: Added 'intIdx', looks for intervals using indexing and memory mapped I/O on the VCF file. Works really fast! Designed to extract a small number of intervals from huge VCF files.<br /> Optimized parsing for VCF files with large number of samples (genotypes).<br /> Option to suppress summary calculation ('-noStats'), can speed up processing considerably in some cases.<br /> Option '-onlyCoding' is set to 'auto' to reduce number of false positives (see next).<br /> Option '-onlyCoding' can be assigne a value: If value is 'true', report only 'protein_coding' transcripts as proteing coding changes. If 'false', report all transcript as if they were conding. Default: Auto, i.e. if transcripts any marked as 'protein_coding' the set it to 'true', if no transcripts are marked as 'protein_coding' then set it to 'false'.<br /> Added BED output format. This is usefull to annotate the output of a Chip-Seq experiment (e.g. after performing peak calling with MACS, you want to know where the peaks hit).

Requirements:	No special requirements
Platforms:	Mac, Mac OSX
Keyword:	Calculation,  Cases,  Considerably,  Genotypes,  Nostats,  Onlycoding,  Option,  Speed,  Summary,  Suppress
Users rating:	0/10