Changes between Version 10 and Version 11 of GoNL_Immunochip_Data_Preparation


Ignore:
Timestamp:
Jul 1, 2011 4:18:18 PM (12 years ago)
Author:
laurent
Comment:

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  • GoNL_Immunochip_Data_Preparation

    v10 v11  
    2727
    2828Once you have the input file, simply run ''fastaFromBed'' on it giving the Human Reference corresponding to the chip data as the other input. For more information on ''fastaFromBed'', see the [http://code.google.com/p/bedtools/ BEDTools] Manual.
     29
     30 * fastaFromBed -fi reference.fa -bed in.bed -fo out.fa.tab -tab
    2931=== Re-arrange Ref/Alt alleles based on the Human Genome Reference ===
    3032Now that we have the Human Reference Genome loci, it is trivial to re-arrange the alleles so that the Ref and Alt alleles correspond to the Human Genome Reference. I wrote a small script, ''align-vcf-to-ref.pl'' that does the work provided the correct input. Note that when flipping the order of alleles in the VCF Ref/Alt columns, one must also flipped the genotypes correctly.