Changes between Version 10 and Version 11 of SOPs/vcf_manipulation


Ignore:
Timestamp:
07/19/16 09:12:32 (9 years ago)
Author:
gbell
Comment:

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  • SOPs/vcf_manipulation

    v10 v11  
    6161}}}
    6262
     63Similar sorts of tasks can be performed with [http://snpeff.sourceforge.net/SnpSift.html#filter SnpSift's filter]  command, like
     64{{{
     65# Get sites where first sample is reference and the second sample is homozygous for the variant
     66cat Variants.vcf | java -jar SnpSift.jar filter "isRef(GEN[0]) & isHom(GEN[1]) & isVariant(GEN[1])" > Selected_variants.vcf
     67}}}
     68
    6369Annotate variants with SNP IDs (if they overlap known SNPs)
    6470{{{