Changes between Version 1 and Version 2 of SOPs/genome_regions_annotations


Ignore:
Timestamp:
03/29/13 14:44:42 (12 years ago)
Author:
gbell
Comment:

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  • SOPs/genome_regions_annotations

    v1 v2  
    9999=== Method 3 (for SNPs, using snpEff) ===
    100100
    101   * This takes SNP positions as input.  I don't think it works on regions > 1 nt.
     101  * This takes SNP positions as input (in VCF format).  I don't think it works on regions > 1 nt.
    102102  * This method has the advantage that it can link SNPs to synonymous and nonsynonymous codons to identify changed in encoded protein.
    103103  * The [[http://snpeff.sourceforge.net/|snpEff web site]] has lots of information.
    … …  
    108108 {{{
    109109# Default output based on Ensembl gene annotation
    110 snpEff hg37.61 snps.calls 1> snps.calls.out.txt 2> snps.calls.err.txt
     110snpEff hg19 < snps.calls.vcf 1> snps.calls.out.txt 2> snps.calls.err.txt
    111111# Default output based on UCSC gene annotation
    112 snpEff hg37 snps.calls 1> snps.calls.out.txt 2> snps.calls.err.txt
     112snpEff hg19 < snps.calls.vcf 1> snps.calls.out.txt 2> snps.calls.err.txt
    113113}}}
    114114
    115115{{{
    116116# Don't show so much stuff
    117 snpEff -no-downstream -no-intergenic -no-intron -no-upstream hg37.61 snps.calls 1> snps.calls.filt.out.txt 2> snps.calls.filt.err.txt
     117snpEff -no-downstream -no-intergenic -no-intron -no-upstream hg19 < snps.calls.vcf 1> snps.calls.filt.out.txt 2> snps.calls.filt.err.txt
    118118}}}
     119
     120On Whitehead servers, pre-installed genomes (with annotations) can be chosen from the directory names in /usr/local/share/snpEff/data