Changes between Version 4 and Version 5 of GoNL_Immunochip_Data_Preparation

Timestamp:

Apr 21, 2011 4:39:41 PM (14 years ago)

Author:

laurent

Comment:

--

GoNL_Immunochip_Data_Preparation

@@ -41 +41 @@
 
 = Liftover file =
-The last step in preparing the immunochip data for comparison with the sequence data is to liftover the VCF file to the same Human Genome Reference as the Sequence data so that comparisons can be made. Here is how: 
+The last step in preparing the immunochip data for comparison with the sequence data is to liftover the VCF file to the same Human Genome Reference as the Sequence data so that comparisons can be made. Here is how:
 
- 1. # Get the appropriate chain files 
+ 1. Get the appropriate chain files
    * From the [ftp://gsapubftp-anonymous@ftp.broadinstitute.org Broad GSA ftp] (password is blank)
-   * From the [http://hgdownload.cse.ucsc.edu/downloads.html#human USCS Genome Browser] # 
- 1. Get the appropriate fasta files (you'll need both from-and-to builds fasta files) 
-   * From [ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ NCBI] 
-   * From [http://hgdownload.cse.ucsc.edu/downloads.html#human USCS Genome Browser] 
- 1. Index the fasta files appropriately to get .fai (samtools) and .dict files (Picard) as described on the [http://www.broadinstitute.org/gsa/wiki/index.php/Preparing_the_essential_GATK_input_files:_the_reference_genome GATK wiki] 
+   * From the [http://hgdownload.cse.ucsc.edu/downloads.html#human USCS Genome Browser] #
+ 1. Get the appropriate fasta files (you'll need both from-and-to builds fasta files)
+   * From [ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ NCBI]
+   * From [http://hgdownload.cse.ucsc.edu/downloads.html#human USCS Genome Browser]
+ 1. Index the fasta files appropriately to get .fai (samtools) and .dict files (Picard) as described on the [http://www.broadinstitute.org/gsa/wiki/index.php/Preparing_the_essential_GATK_input_files:_the_reference_genome GATK wiki]
  1. Get and run the [http://www.broadinstitute.org/gsa/wiki/index.php/LiftOverVCF.pl GATK LiftOver tool]
 
-Note that once the liftover VCF has successfully been created, it can be used to liftover the PLINK files. To do so: 
+Note that once the liftover VCF has successfully been created, it can be used to liftover the PLINK files. To do so:
 
- 1. Remove all SNPs that are not present in the new reference VCF file (using plink --extract) 
+ 1. Remove all SNPs that are not present in the new reference VCF file (using plink --extract)
  1. Use the liftover VCF as an input to the ''liftover-bim.pl'' tool .