Hapmap3 in hg19/GRCh37 plink format PED and MAP

Question

[Shicheng Guo]

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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[Kevin Blighe]

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

[Shicheng Guo]

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

[marcella.devoto]

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

[Shicheng Guo]

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

[pately]

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

[Shicheng Guo]

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

Answer 1

[melissawongukm]

Thanks for the files. It was a pain to download them from Baidu. They are now available on my dropbox at https://www.dropbox.com/sh/ycvtoner1d2bujs/AACtKzZwsL9ln0vI5Fnxuof0a?dl=0