Question: Hapmap 3 in hg19/GRCh37 plink format PED and MAP
3
gravatar for Shicheng Guo
12 months ago by
Shicheng Guo7.4k
Shicheng Guo7.4k wrote:

Any one have hg19 map for hapmap 3 ped file?

I downloaded the hapmap 3 data from following link. I think some formal download service can be provided since all of us will use it, right?

https://www.broadinstitute.org/files/shared/mpg/hapmap3/hapmap3_r1_b36_fwd_consensus.qc.poly.recode.map.bz2

they only provided hg18 ped and map files. So I transfer hg18 map to hg19 map with lifeOver and trim plink again.

wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/liftOver
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg18/liftOver/hg18ToHg19.over.chain.gz
plink --bfile hapmap3_r1_b36_fwd_consensus.qc.poly.recode  --recode --tab --out hapmap3_r1_b36_fwd_consensus.qc.poly.recode
awk '{print "chr"$1,"\t",$4,"\t",$4+1,"\t",$2}' hapmap3_r1_b36_fwd_consensus.qc.poly.recode.map > hapmap3.hg18.bed
./liftOver hapmap3.hg18.bed hg18ToHg19.over.chain.gz hapmap3.hg19.bed unmap
awk '{print $1,"\t",$4,"\t",0,"\t",$2}' hapmap3.hg19.bed > hapmap3_r1_b37_fwd_consensus.qc.poly.recode.map
perl -p -i -e 's/chr//g' hapmap3_r1_b37_fwd_consensus.qc.poly.recode.map
mv hapmap3_r1_b36_fwd_consensus.qc.poly.recode.ped hapmap3_r1_b37_fwd_consensus.qc.poly.recode.ped
plink --file hapmap3_r1_b37_fwd_consensus.qc.poly.recode --make-bed --out hapmap3_r1_b37_fwd_consensus.qc.poly.recode

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Anyone who is interesting in hapmap 3 hg19 based plink files (ped, map and binary form: fam, bim, bed) can download from this link:

https://pan.baidu.com/s/1ElJ-heuW9jZXDeU9R-dZqg

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hg19 ped map hg18 hapmap 3 • 1.1k views
ADD COMMENTlink modified 6 weeks ago • written 12 months ago by Shicheng Guo7.4k
1

Sorry, is this more a 'News' item and not really a question? There also appears to be a link missing from your post.

ADD REPLYlink written 12 months ago by Kevin Blighe39k
4

In the beginning it is a question. But no body answer me. Finally, I solve the problem and show the method and result.

ADD REPLYlink written 12 months ago by Shicheng Guo7.4k

Sorry where is the link to download the HapMap3 in hg19?

ADD REPLYlink written 11 months ago by marcella.devoto0
1

Sorry. Format to insert the link, please download the data and related files from the following link:

https://pan.baidu.com/s/1ElJ-heuW9jZXDeU9R-dZqg

ADD REPLYlink written 11 months ago by Shicheng Guo7.4k

Hi. Can you upload the hg19 plink binaries to google drive or dropbox? I cannot access the files via Baidu. Thank you.

ADD REPLYlink written 6 weeks ago by pately0

Our hospital internet blocked google drive and dropbox. I cannot use dropbox..

ADD REPLYlink written 6 weeks ago by Shicheng Guo7.4k
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