This page contains the plink format
files for updating TOP strand data to the listed build. Each zip file
contains 3 files,
HumanHap550-2v3_B-bXX.chr.txt,
HumanHap550-2v3_B-bXX.pos.txt
and
HumanHap550-2v3_B-bXX.minus_strand_list.txt
Where XX is the build of the files.
The .chr.txt and .pos.txt files contain in plink format the
chromosome and positions for SNPs on the chip and these are strand
independent. The .minus_strand_list.txt contains a single list of SNP
ids that can be used to update the strand to the forward strand, this
is dependant on you knowing the current strand of your data, files on
this page assume it is the TOP strand.
The procedure for using these files in plink is as below
(a)
Remove variants that do not map to the genome.
plink
--bfile DATA.b36
--extract HumanHap550-2v3_B-b37.chr.txt --out DATA.update1 --make-bed
(b)
Flip the orientation of all variants not aligned
to the forward DNA strand.
plink
--bfile
DATA.update1 --flip HumanHap550-2v3_B-b37.minus_strand_list.txt --out
DATA.update2
--make-bed
(c)
Update the chromosome and position of all
variants to build 37.
plink
--bfile
DATA.update2 --update-map HumanHap5500-2v3_B-b37.pos.txt --out
DATA.update3
--make-bed
plink
--bfile
DATA.update3 --update-map HumanHap550-2v3_B-b37.chr.txt --update-chr
--out DATA.b37
--make-bed
Files:
Build 37 TOP Strand files
HumanHap550-2v3_B-b37.zip