Changes between Version 10 and Version 11 of SOPs/callingSNPs


Ignore:
Timestamp:
01/16/14 16:09:53 (10 years ago)
Author:
gbell
Comment:

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  • SOPs/callingSNPs

    v10 v11  
    2929== Filtering SNPs ==
    3030
    31   * Remove, or retrieve, known SNPs
    32 
    33 
    34 {{{
    35   #To remove known SNPs, use intersectBed (bedtools).  Known SNPs can be downloaded from Ensembl or NCBI/UCSC (eg. dbSNP)
    36   intersectBed -a accepted_hits.raw.filtered.vcf -b Mus_musculus.NCBIM37.60.bed -wo > filteredSNPs.vcf
    37 }}}
    38 
     31  * See [wiki:SOPs/variant_calling Add filters and annotations to raw variants].
    3932 
    4033== Annotating SNPs ==