Changes between Version 7 and Version 8 of GoNL_Immunochip_Data_Preparation

Timestamp:

May 3, 2011 11:37:45 AM (14 years ago)

Author:

laurent

Comment:

--

GoNL_Immunochip_Data_Preparation

@@ -51 +51 @@
  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]
+ 1. IMPORTANT: Check your VCF file header as some versions of the GATK liftover tool (e.g. v1.0.5083) might mix the individuals in the header (sort alphabetically rather than preserve original order). If the order is changed, then you should copy/paste the original order from the source VCF file.
 
 Note that once the liftover VCF has successfully been created, it can be used to liftover the PLINK files. To do so:
@@ -56 +57 @@
  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 .
-
 == Downloads ==
 All tools developed inhouse at UMCG are available here: [[http://www.bbmriwiki.nl/svn/ped_to_vcf]]