Changes between Version 11 and Version 12 of SOPs/vcf


Ignore:
Timestamp:
10/28/13 10:33:55 (11 years ago)
Author:
gbell
Comment:

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  • SOPs/vcf

    v11 v12  
    6969|| SP || Phred-scaled strand bias P-value || ||
    7070|| PL || List of Phred-scaled genotype likelihoods || Scores for 0/0 (homozygous ref), 0/1/ (heterozygous), and 1/1 (homozygous alt) ||
     71
     72== Predicting the effects of a set of variants ==
     73
     74Especially for genome-wide analyses, often the most difficult is prioritizing and making biological sense of a potentially very long list of variants.
     75
     76The best way(s) to do this often depends on the goal of the study, but it may help to use tools such as
     77
     78* snpEff
     79   * Given a genome-wide gene annotation file (as a GTF file), each variant can be linked to an exon, intron, and/or intergenic region.
     80   * For variants within an open reading frame, snpEff will determine the relevant amino acid and if the variant will produce a synonymous or non-synonymous change.
     81   * Example command: java -jar /usr/local/share/snpEff/snpEff.jar -c /usr/local/share/snpEff/snpEff.config GENOME < Variants.vcf > Variants.snpEff.vcf
     82     * where GENOME is chosen from those listed with the command java -jar /usr/local/share/snpEff/snpEff.jar databases
     83* Ensembl's Variant Effect Predictor
     84   * Go to http://www.ensembl.org/info/docs/tools/vep/index.html and click on "Launch the online VEP tool!".