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Documentation for the ANNOVAR software
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personalized "gwasCatalog" in ANNOVAR #138

Open Shicheng-Guo opened 3 years ago

Shicheng-Guo commented 3 years ago

Dear Prof. Wang,

I meet an trouble to prepare gwasCatalog similar format files. I downloaded gwasCatalog from gwasCatalog website, rather than UCSC and then reformat it as "chr\tstart\tend\anno", however, the performance of this file have difference with ANNOVAR prepared gwasCatalog. I find the file you prepared works well, while my version doesn't. do you have any suggestion? Thanks.

Here is my gwascatalog

1       845016  845017  Morning vs. evening chronotype(B=2.16,MLOG=7.40)
1       959192  959193  Pancreatic cancer(B=1.26,MLOG=13.10)
1       960325  960326  Heel bone mineral density(B=0.00,MLOG=12.30),Heel bone mineral density(B=0.02,MLOG=12.40),Heel bone mineral density(B=0.03,MLOG=16.10)
1       962485  962486  Lysophosphatidylethanolamine levels(B=0.87,MLOG=7.40)
1       965138  965139  Anorectal malformation(B=0.00,MLOG=12.00)
1       973928  973929  Height(B=0.02,MLOG=7.05)
1       989147  989148  Apolipoprotein A1 levels(B=0.01,MLOG=10.70)
1       999841  999842  HDL cholesterol levels(B=0.01,MLOG=10.00)
1       1008087 1008088 Blood protein levels(B=0.74,MLOG=11.70)
1       1014862 1014863 Blood protein levels(B=0.26,MLOG=24.00)
1       1023572 1023573 Height(B=0.00,MLOG=11.70)

Here is ANNOVAR prepared gwasCatalog 

591     chr1    832872  832873  rs2977608       31969693        Coleman JRI     2020-01-23      Mol Psychiatry  Genome-wide gene-environment analyses of major depressive disorder and reported lifetime traumatic experiences in UK Biobank>
591     chr1    845016  845017  rs141175086     26955885        Lane JM 2016-03-09      Nat Commun      Genome-wide association analysis identifies novel loci for chronotype in 100,420 individuals from the UK Biobank.       Morning vs. >
592     chr1    946652  946653  rs2272756       30895295        Jonnalagadda M  2019-03-21      Genome Biol Evol        A genome-wide association study of skin and iris pigmentation among individuals of South Asian ancestry.        Skin>
592     chr1    959138  959139  rs115438739     31596458        Greenwood TA    2019-10-09      JAMA Psychiatry Genome-wide Association of Endophenotypes for Schizophrenia From the Consortium on the Genetics of Schizophrenia (COGS) Stud>
592     chr1    959192  959193  rs13303010      29422604        Klein AP        2018-02-08      Nat Commun      Genome-wide meta-analysis identifies five new susceptibility loci for pancreatic cancer.        Pancreatic cancer(B=1.26,P=8>
592     chr1    960325  960326  rs13303327      30598549        Morris JA       2018-12-31      Nat Genet       An atlas of genetic influences on osteoporosis in humans and mice.      Heel bone mineral density(B=0.02,P=4E-13)       426,>
592     chr1    960325  960326  rs13303327      30595370        Kichaev G       2018-12-27      Am J Hum Genet  Leveraging Polygenic Functional Enrichment to Improve GWAS Power.       Heel bone mineral density(B=0.00,P=5E-13)       appr>
592     chr1    960325  960326  rs13303327      30048462        Kim SK  2018-07-26      PLoS One        Identification of 613 new loci associated with heel bone mineral density and a polygenic risk score for bone mineral density, osteop>
5
kaichop commented 3 years ago

I suggest that you use the ucsc version which is already processed. It may be less updated, but it is preformatted.

On Wed, May 19, 2021 at 10:45 AM Shicheng Guo @.***> wrote:

Dear Prof. Wang,

I meet an trouble to prepare gwasCatalog similar format files. I downloaded gwasCatalog from gwasCatalog website, rather than UCSC and then reformat it as "chr\tstart\tend\anno", however, the performance of this file have difference with ANNOVAR prepared gwasCatalog. I find the file you prepared works well, while my version doesn't. do you have any suggestion? Thanks.

Here is my gwascatalog

1 845016 845017 Morning vs. evening chronotype(B=2.16,MLOG=7.40) 1 959192 959193 Pancreatic cancer(B=1.26,MLOG=13.10) 1 960325 960326 Heel bone mineral density(B=0.00,MLOG=12.30),Heel bone mineral density(B=0.02,MLOG=12.40),Heel bone mineral density(B=0.03,MLOG=16.10) 1 962485 962486 Lysophosphatidylethanolamine levels(B=0.87,MLOG=7.40) 1 965138 965139 Anorectal malformation(B=0.00,MLOG=12.00) 1 973928 973929 Height(B=0.02,MLOG=7.05) 1 989147 989148 Apolipoprotein A1 levels(B=0.01,MLOG=10.70) 1 999841 999842 HDL cholesterol levels(B=0.01,MLOG=10.00) 1 1008087 1008088 Blood protein levels(B=0.74,MLOG=11.70) 1 1014862 1014863 Blood protein levels(B=0.26,MLOG=24.00) 1 1023572 1023573 Height(B=0.00,MLOG=11.70)

Here is ANNOVAR prepared gwasCatalog

591 chr1 832872 832873 rs2977608 31969693 Coleman JRI 2020-01-23 Mol Psychiatry Genome-wide gene-environment analyses of major depressive disorder and reported lifetime traumatic experiences in UK Biobank> 591 chr1 845016 845017 rs141175086 26955885 Lane JM 2016-03-09 Nat Commun Genome-wide association analysis identifies novel loci for chronotype in 100,420 individuals from the UK Biobank. Morning vs. > 592 chr1 946652 946653 rs2272756 30895295 Jonnalagadda M 2019-03-21 Genome Biol Evol A genome-wide association study of skin and iris pigmentation among individuals of South Asian ancestry. Skin> 592 chr1 959138 959139 rs115438739 31596458 Greenwood TA 2019-10-09 JAMA Psychiatry Genome-wide Association of Endophenotypes for Schizophrenia From the Consortium on the Genetics of Schizophrenia (COGS) Stud> 592 chr1 959192 959193 rs13303010 29422604 Klein AP 2018-02-08 Nat Commun Genome-wide meta-analysis identifies five new susceptibility loci for pancreatic cancer. Pancreatic cancer(B=1.26,P=8> 592 chr1 960325 960326 rs13303327 30598549 Morris JA 2018-12-31 Nat Genet An atlas of genetic influences on osteoporosis in humans and mice. Heel bone mineral density(B=0.02,P=4E-13) 426,> 592 chr1 960325 960326 rs13303327 30595370 Kichaev G 2018-12-27 Am J Hum Genet Leveraging Polygenic Functional Enrichment to Improve GWAS Power. Heel bone mineral density(B=0.00,P=5E-13) appr> 592 chr1 960325 960326 rs13303327 30048462 Kim SK 2018-07-26 PLoS One Identification of 613 new loci associated with heel bone mineral density and a polygenic risk score for bone mineral density, osteop> 5

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Shicheng-Guo commented 3 years ago

Agree. Now I need to prepare some personal gwas resource into ANNOVAR DB. I feel the format I prepared not works well and I don't know how to make the format as UCSC (the 1st column is bin, I think). Do you have any suggestion?

Thanks. Shicheng

I suggest that you use the ucsc version which is already processed. It may be less updated, but it is preformatted. … On Wed, May 19, 2021 at 10:45 AM Shicheng Guo @.***> wrote: Dear Prof. Wang, I meet an trouble to prepare gwasCatalog similar format files. I downloaded gwasCatalog from gwasCatalog website, rather than UCSC and then reformat it as "chr\tstart\tend\anno", however, the performance of this file have difference with ANNOVAR prepared gwasCatalog. I find the file you prepared works well, while my version doesn't. do you have any suggestion? Thanks. Here is my gwascatalog 1 845016 845017 Morning vs. evening chronotype(B=2.16,MLOG=7.40) 1 959192 959193 Pancreatic cancer(B=1.26,MLOG=13.10) 1 960325 960326 Heel bone mineral density(B=0.00,MLOG=12.30),Heel bone mineral density(B=0.02,MLOG=12.40),Heel bone mineral density(B=0.03,MLOG=16.10) 1 962485 962486 Lysophosphatidylethanolamine levels(B=0.87,MLOG=7.40) 1 965138 965139 Anorectal malformation(B=0.00,MLOG=12.00) 1 973928 973929 Height(B=0.02,MLOG=7.05) 1 989147 989148 Apolipoprotein A1 levels(B=0.01,MLOG=10.70) 1 999841 999842 HDL cholesterol levels(B=0.01,MLOG=10.00) 1 1008087 1008088 Blood protein levels(B=0.74,MLOG=11.70) 1 1014862 1014863 Blood protein levels(B=0.26,MLOG=24.00) 1 1023572 1023573 Height(B=0.00,MLOG=11.70) Here is ANNOVAR prepared gwasCatalog 591 chr1 832872 832873 rs2977608 31969693 Coleman JRI 2020-01-23 Mol Psychiatry Genome-wide gene-environment analyses of major depressive disorder and reported lifetime traumatic experiences in UK Biobank> 591 chr1 845016 845017 rs141175086 26955885 Lane JM 2016-03-09 Nat Commun Genome-wide association analysis identifies novel loci for chronotype in 100,420 individuals from the UK Biobank. Morning vs. > 592 chr1 946652 946653 rs2272756 30895295 Jonnalagadda M 2019-03-21 Genome Biol Evol A genome-wide association study of skin and iris pigmentation among individuals of South Asian ancestry. Skin> 592 chr1 959138 959139 rs115438739 31596458 Greenwood TA 2019-10-09 JAMA Psychiatry Genome-wide Association of Endophenotypes for Schizophrenia From the Consortium on the Genetics of Schizophrenia (COGS) Stud> 592 chr1 959192 959193 rs13303010 29422604 Klein AP 2018-02-08 Nat Commun Genome-wide meta-analysis identifies five new susceptibility loci for pancreatic cancer. Pancreatic cancer(B=1.26,P=8> 592 chr1 960325 960326 rs13303327 30598549 Morris JA 2018-12-31 Nat Genet An atlas of genetic influences on osteoporosis in humans and mice. Heel bone mineral density(B=0.02,P=4E-13) 426,> 592 chr1 960325 960326 rs13303327 30595370 Kichaev G 2018-12-27 Am J Hum Genet Leveraging Polygenic Functional Enrichment to Improve GWAS Power. Heel bone mineral density(B=0.00,P=5E-13) appr> 592 chr1 960325 960326 rs13303327 30048462 Kim SK 2018-07-26 PLoS One Identification of 613 new loci associated with heel bone mineral density and a polygenic risk score for bone mineral density, osteop> 5 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#138>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OGE3E7WC2GMYG5QBRLTOPFITANCNFSM45E2XHNA .

kaichop commented 3 years ago

The easiest way is to just create a BED file yourself. No need to create the same format as UCSC. Then in annovar you use bed as dbtype.

On Wed, May 19, 2021 at 12:05 PM Shicheng Guo @.***> wrote:

Agree. Now I need to prepare some personal gwas resource into ANNOVAR DB. I feel the format I prepared not works well and I don't know how to make the format as UCSC (the 1st column is bin, I think). Do you have any suggestion?

Thanks. Shicheng

I suggest that you use the ucsc version which is already processed. It may be less updated, but it is preformatted. … <#m5795240229028440502> On Wed, May 19, 2021 at 10:45 AM Shicheng Guo @.***> wrote: Dear Prof. Wang, I meet an trouble to prepare gwasCatalog similar format files. I downloaded gwasCatalog from gwasCatalog website, rather than UCSC and then reformat it as "chr\tstart\tend\anno", however, the performance of this file have difference with ANNOVAR prepared gwasCatalog. I find the file you prepared works well, while my version doesn't. do you have any suggestion? Thanks. Here is my gwascatalog 1 845016 845017 Morning vs. evening chronotype(B=2.16,MLOG=7.40) 1 959192 959193 Pancreatic cancer(B=1.26,MLOG=13.10) 1 960325 960326 Heel bone mineral density(B=0.00,MLOG=12.30),Heel bone mineral density(B=0.02,MLOG=12.40),Heel bone mineral density(B=0.03,MLOG=16.10) 1 962485 962486 Lysophosphatidylethanolamine levels(B=0.87,MLOG=7.40) 1 965138 965139 Anorectal malformation(B=0.00,MLOG=12.00) 1 973928 973929 Height(B=0.02,MLOG=7.05) 1 989147 989148 Apolipoprotein A1 levels(B=0.01,MLOG=10.70) 1 999841 999842 HDL cholesterol levels(B=0.01,MLOG=10.00) 1 1008087 1008088 Blood protein levels(B=0.74,MLOG=11.70) 1 1014862 1014863 Blood protein levels(B=0.26,MLOG=24.00) 1 1023572 1023573 Height(B=0.00,MLOG=11.70) Here is ANNOVAR prepared gwasCatalog 591 chr1 832872 832873 rs2977608 31969693 Coleman JRI 2020-01-23 Mol Psychiatry Genome-wide gene-environment analyses of major depressive disorder and reported lifetime traumatic experiences in UK Biobank> 591 chr1 845016 845017 rs141175086 26955885 Lane JM 2016-03-09 Nat Commun Genome-wide association analysis identifies novel loci for chronotype in 100,420 individuals from the UK Biobank. Morning vs. > 592 chr1 946652 946653 rs2272756 30895295 Jonnalagadda M 2019-03-21 Genome Biol Evol A genome-wide association study of skin and iris pigmentation among individuals of South Asian ancestry. Skin> 592 chr1 959138 959139 rs115438739 31596458 Greenwood TA 2019-10-09 JAMA Psychiatry Genome-wide Association of Endophenotypes for Schizophrenia From the Consortium on the Genetics of Schizophrenia (COGS) Stud> 592 chr1 959192 959193 rs13303010 29422604 Klein AP 2018-02-08 Nat Commun Genome-wide meta-analysis identifies five new susceptibility loci for pancreatic cancer. Pancreatic cancer(B=1.26,P=8> 592 chr1 960325 960326 rs13303327 30598549 Morris JA 2018-12-31 Nat Genet An atlas of genetic influences on osteoporosis in humans and mice. Heel bone mineral density(B=0.02,P=4E-13) 426,> 592 chr1 960325 960326 rs13303327 30595370 Kichaev G 2018-12-27 Am J Hum Genet Leveraging Polygenic Functional Enrichment to Improve GWAS Power. Heel bone mineral density(B=0.00,P=5E-13) appr> 592 chr1 960325 960326 rs13303327 30048462 Kim SK 2018-07-26 PLoS One Identification of 613 new loci associated with heel bone mineral density and a polygenic risk score for bone mineral density, osteop> 5 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <

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