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Documentation for the ANNOVAR software
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"chr1" vs "1" in annotation file #139

Open Shicheng-Guo opened 3 years ago

Shicheng-Guo commented 3 years ago

Dear Prof. Wang,

I notice some annotation use "chr1" while others use '1' to represent chromosome. Is there any rule to determine how to select the style?

Here is example for "chr1"

==> hg38_gwasCatalog.txt <==
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.Major depressive disorder(B=1.07,P=8E-6)        29,475 European ancestry cases, 63,482 European ancestry controls       NA      1p36.33 NR      rs2977608-A     0.259029        8E-6            1.0729614       [1.04-1.1]      Affymetrix [7791636] (imputed)       N
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. evening chronotype(B=2.16,P=4E-8)        8,724 European ancestry evening chronotype individuals, 26,948 European ancestry morning chronotype individuals NA      1p36.33 LINC01128       rs141175086-C   0.998   4E-8            2.16    [1.34-3.49]  Affymetrix [73355677] (imputed) N
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 reflectance (Melanin index)(B=0.32,P=3E-6)      720 South Asian ancestry individuals            1p36.33 NR      rs2272756-A     NR      3E-6            0.324533        [0.19-0.46] unit increase       Affymetrix, Illumina [at least 398118] (imputed)     N
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) Study.       California verbal learning test score(B=7.54,P=7E-6)    523 European ancestry schizophrenia cases, 100 Latino schizophrenia cases, 827 European ancestry controls, 83 Latino controls   NA      1p36.33 NOC2L   rs115438739-A   NR  7E-6             7.540324        [4.4-10.69] unit increase       Illumina [> 6200000] (imputed)  N
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=8E-14)    9,040 European ancestry cases, 12,496 European ancestry controls        up to 2,737 cases, up to 4,752 controls 1p36.33 NOC2L   rs13303010-G    0.11    8E-14           1.26    [1.19-1.35]     Illumina [11381182] (imputed)   N
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)       426,824 British ancestry individuals NA      1p36.33 KLHL17  rs13303327-G    0.0857658       4E-13           0.0237969       [0.017-0.03] unit increase      NR [13737936] (imputed) N
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)       approximately 446,000 European ancestry individuals  NA      1p36.33         rs13303327-?    NR      5E-13                           NR [~ 8900000] (imputed)        N
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, osteoporosis and fracture.     Heel bone mineral density(B=0.03,P=8E-17)       394,929 European ancestry individuals   NA      1p36.33         rs13303327-?    NR      8E-17           0.0289903       [0.022-0.036] unit increase     Affymetrix [20259828] (imputed)      N
592     chr1    962485  962486  rs201385366     31551469        Tabassum R      2019-09-24      Nat Commun      Genetic architecture of human plasma lipidome and its link to cardiovascular disease.   Lysophosphatidylethanolamine levels(B=0.87,P=4E-8)   2,045 European ancestry individuals     NA      1p36.33 KLHL17  rs201385366-T   NR      4E-8    (LPE(22:6;0))   0.8736  [0.56-1.18] unit decrease       Illumina [~ 9300000] (imputed)  N
592     chr1    965138  965139  rs140019196     31136621        van de Putte R  2019-05-28      PLoS One        Exome chip association study excluded the involvement of rare coding variants with large effect sizes in the etiology of anorectal malformations.    Anorectal malformation(B=0.00,P=1E-12)  568 European ancestry cases, 1,860 European ancestry controls   NA      1p36.33 KLHL17  rs140019196-G   0.0     1E-12                           Illumina [239042]       N

Thanks.

Shicheng

kaichop commented 3 years ago

There is no rule, to be compatible to all different annotation databases, chr is optional. Many old databases use "chr1" even though the official reference genome says "1", because 3rd party data producers (for example ucsc) compile their own version of reference genome.

On Wed, May 19, 2021 at 10:59 AM Shicheng Guo @.***> wrote:

Dear Prof. Wang,

I notice some annotation use "chr1" while others use '1' to represent chromosome. Is there any rule to determine how to select the style?

Here is example for "chr1"

==> hg38_gwasCatalog.txt <== 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.Major depressive disorder(B=1.07,P=8E-6) 29,475 European ancestry cases, 63,482 European ancestry controls NA 1p36.33 NR rs2977608-A 0.259029 8E-6 1.0729614 [1.04-1.1] Affymetrix [7791636] (imputed) N 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. evening chronotype(B=2.16,P=4E-8) 8,724 European ancestry evening chronotype individuals, 26,948 European ancestry morning chronotype individuals NA 1p36.33 LINC01128 rs141175086-C 0.998 4E-8 2.16 [1.34-3.49] Affymetrix [73355677] (imputed) N 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 reflectance (Melanin index)(B=0.32,P=3E-6) 720 South Asian ancestry individuals 1p36.33 NR rs2272756-A NR 3E-6 0.324533 [0.19-0.46] unit increase Affymetrix, Illumina [at least 398118] (imputed) N 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) Study. California verbal learning test score(B=7.54,P=7E-6) 523 European ancestry schizophrenia cases, 100 Latino schizophrenia cases, 827 European ancestry controls, 83 Latino controls NA 1p36.33 NOC2L rs115438739-A NR 7E-6 7.540324 [4.4-10.69] unit increase Illumina [> 6200000] (imputed) N 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=8E-14) 9,040 European ancestry cases, 12,496 European ancestry controls up to 2,737 cases, up to 4,752 controls 1p36.33 NOC2L rs13303010-G 0.11 8E-14 1.26 [1.19-1.35] Illumina [11381182] (imputed) N 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) 426,824 British ancestry individuals NA 1p36.33 KLHL17 rs13303327-G 0.0857658 4E-13 0.0237969 [0.017-0.03] unit increase NR [13737936] (imputed) N 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) approximately 446,000 European ancestry individuals NA 1p36.33 rs13303327-? NR 5E-13 NR [~ 8900000] (imputed) N 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, osteoporosis and fracture. Heel bone mineral density(B=0.03,P=8E-17) 394,929 European ancestry individuals NA 1p36.33 rs13303327-? NR 8E-17 0.0289903 [0.022-0.036] unit increase Affymetrix [20259828] (imputed) N 592 chr1 962485 962486 rs201385366 31551469 Tabassum R 2019-09-24 Nat Commun Genetic architecture of human plasma lipidome and its link to cardiovascular disease. Lysophosphatidylethanolamine levels(B=0.87,P=4E-8) 2,045 European ancestry individuals NA 1p36.33 KLHL17 rs201385366-T NR 4E-8 (LPE(22:6;0)) 0.8736 [0.56-1.18] unit decrease Illumina [~ 9300000] (imputed) N 592 chr1 965138 965139 rs140019196 31136621 van de Putte R 2019-05-28 PLoS One Exome chip association study excluded the involvement of rare coding variants with large effect sizes in the etiology of anorectal malformations. Anorectal malformation(B=0.00,P=1E-12) 568 European ancestry cases, 1,860 European ancestry controls NA 1p36.33 KLHL17 rs140019196-G 0.0 1E-12 Illumina [239042] N

Thanks.

Shicheng

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