Changes between Version 14 and Version 15 of GoNL_Immunochip_Data_Preparation
- Timestamp:
- Feb 13, 2012 2:30:43 PM (12 years ago)
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GoNL_Immunochip_Data_Preparation
v14 v15 25 25 26 26 * From VCF: grep -v '!^#' in.vcf | awk '{OFS="\t";print $1,$2,$2+1}' > out.bed 27 * OR (depending on the ref seq) From VCF: grep -v '!^#' in.vcf | awk '{OFS="\t";print $1,$2-1,$2}' > out.bed 27 28 28 29 Once 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.
